Gene Set Pathway and Network Analysis by Using GSEA, Cytoscape and Enrichment Map

Loading Packages and Data From A2

if (!require("knitr", quietly = TRUE))
  install.packages("knitr")
if (!require("RSQLite", quietly = TRUE)){
  install.packages("RSQLite")
}

library(knitr)
library(RSQLite)
load("A3.RData")

The ranked gene list from A2 is shown below. There are multiple parameters that can be selected. We selected to use the up-regulated rank by logFC. Original data GSE_150392 can be downloaded from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE150392

knitr::kable(MultipuleRank, caption = 'Table 1. Ranked Gene list by logFC Up-Regulated')

Table 1. Ranked Gene list by logFC Up-Regulated

Gene	logFC	logCPM	F	PValue	FDR
PGAM2	-5.823109	5.602283	114.57596	0.0000032	0.0012769
KCNIP2	-5.719563	4.086743	160.76552	0.0000007	0.0007268
MYL2	-5.499684	10.723374	108.19050	0.0000040	0.0012869
FBXL22	-5.289779	3.678330	113.60661	0.0000033	0.0012869
ALAS2	-5.044219	5.316813	210.75460	0.0000002	0.0007000
METTL7B	-4.984911	3.734938	68.29247	0.0000241	0.0024364
HHATL	-4.724839	4.224531	108.70331	0.0000039	0.0012869
ACTA1	-4.549569	7.045206	63.09443	0.0000326	0.0027663
FXYD1	-4.430060	5.376322	55.46745	0.0000529	0.0032675
SPC25	-4.366327	2.902875	43.86371	0.0001256	0.0052210
FAM111B	-4.336571	2.874277	102.56547	0.0000044	0.0012883
LINC02502	-4.298162	2.405372	24.32000	0.0009597	0.0161242
TNNC1	-4.285373	9.436908	94.52402	0.0000068	0.0014874
IRX4-AS1	-4.282455	2.134377	20.00454	0.0017844	0.0229872
COX6A2	-4.168300	2.086863	25.38949	0.0008339	0.0148626
PBK	-4.114213	3.718915	170.56504	0.0000005	0.0007127
TCAP	-4.067439	6.552621	80.76739	0.0000126	0.0017434
CENPM	-4.064744	3.126273	42.12308	0.0001454	0.0056996
MSS51	-4.049343	3.683218	103.53421	0.0000047	0.0012904
TMSB15A	-4.023837	3.743561	37.09184	0.0002289	0.0074975
TNMD	-4.017588	5.303521	89.96110	0.0000083	0.0015101
MAOB	-4.013483	2.448577	65.21380	0.0000287	0.0026349
S100A8	-3.987699	1.883211	20.61993	0.0016239	0.0217399
ADPRHL1	-3.938632	5.307378	158.94060	0.0000007	0.0007268
MYL7	-3.935387	12.710147	65.20630	0.0000287	0.0026349
ODAM	-3.875695	1.766859	30.72430	0.0018866	0.0238249
CKMT2	-3.843017	6.214901	138.62454	0.0000013	0.0008940
CCDC34	-3.807975	5.223245	66.11307	0.0000273	0.0025570
TROAP	-3.795809	2.443732	84.78398	0.0000090	0.0015377
FGF12	-3.795245	6.805036	156.87407	0.0000007	0.0007268
ACE2	-3.792261	3.553994	22.73039	0.0011935	0.0182253
MYL4	-3.789321	10.195632	76.73172	0.0000154	0.0019481
NME5	-3.772923	2.783836	48.77469	0.0000852	0.0041860
HSPB7	-3.772049	10.052815	166.34553	0.0000006	0.0007127
CPNE5	-3.696151	5.992740	171.99675	0.0000005	0.0007127
CORIN	-3.695186	6.589812	61.16965	0.0000366	0.0028743
RAD51AP1	-3.668636	2.661695	104.40286	0.0000039	0.0012869
SUSD2	-3.664531	3.047584	46.43830	0.0001020	0.0046244
NAV2-AS2	-3.659570	5.527039	60.34002	0.0000386	0.0029093
TNNI1	-3.649594	10.687197	83.04644	0.0000113	0.0016217
GJD2	-3.648797	2.004456	64.36838	0.0005406	0.0116472
LDB3	-3.633489	7.996646	144.52753	0.0000010	0.0008348
GINS2	-3.632645	3.427047	75.81022	0.0000161	0.0019774
PCLAF	-3.618731	3.518891	31.51488	0.0004036	0.0100969
MYLK-AS1	-3.614126	3.636269	25.19938	0.0008547	0.0150415
ACTC1	-3.599775	13.373242	95.08687	0.0000057	0.0014052
MIR133A1HG	-3.586468	3.376682	55.81417	0.0000517	0.0032300
LINC01611	-3.581984	2.196025	20.81456	0.0015769	0.0214442
LDHD	-3.576655	2.728602	102.45834	0.0000042	0.0012883
LINC01182	-3.561014	2.109034	21.69740	0.0013837	0.0199363
SLC35D3	-3.553160	1.849767	65.26468	0.0019145	0.0240364
CD36	-3.544471	5.422586	121.37468	0.0000022	0.0011591
MB	-3.542870	7.055788	97.04714	0.0000061	0.0014197
MARCHF11	-3.530975	3.912894	59.83615	0.0000398	0.0029469
FABP3	-3.492141	9.278923	59.86107	0.0000397	0.0029469
TNNI3	-3.479622	9.576369	58.99188	0.0000420	0.0030190
C1QL1	-3.445765	4.228980	53.15605	0.0000620	0.0035473
MYH7	-3.415903	11.653417	21.54393	0.0014151	0.0202251
HSPB3	-3.409678	6.944682	64.26989	0.0000304	0.0026939
LMOD2	-3.403714	6.089989	142.83660	0.0000011	0.0008348
SMPX	-3.395799	7.962930	59.92075	0.0000396	0.0029469
GPD1	-3.377976	2.085860	75.09594	0.0005304	0.0115514
DLGAP5	-3.375682	3.879891	72.90729	0.0000187	0.0021763
ATP6V1G2	-3.357918	2.813120	35.17433	0.0002758	0.0083139
AURKB	-3.351708	3.019736	51.41282	0.0000702	0.0037726
CDKN3	-3.334427	3.629323	39.82371	0.0001778	0.0065217
CENPU	-3.303800	4.258795	114.11012	0.0000027	0.0012769
TRIM54	-3.298866	3.697847	93.65253	0.0000064	0.0014424
FITM1	-3.291142	6.445232	45.38724	0.0001109	0.0048176
OIP5	-3.282617	2.587212	64.26485	0.0000292	0.0026381
FSD2	-3.274605	4.403858	46.69062	0.0001000	0.0045547
NDC80	-3.269491	3.617126	87.75540	0.0000086	0.0015265
CHCHD10	-3.261912	4.051329	37.10621	0.0002286	0.0074975
FAM133A	-3.237091	1.828973	31.89990	0.0035706	0.0351559
DMAC1	-3.234254	5.058723	50.98336	0.0000724	0.0038494
KLHDC9	-3.218902	2.751979	39.92567	0.0001762	0.0065139
PPP1R1A	-3.171572	5.119336	66.15034	0.0000272	0.0025570
LSMEM2	-3.164595	4.363786	59.04122	0.0000419	0.0030190
SPSB4	-3.155675	3.233936	56.20985	0.0000503	0.0031761
NUF2	-3.151356	2.999939	89.38433	0.0000073	0.0015101
TESC	-3.150083	4.749327	76.28222	0.0000157	0.0019675
CALN1	-3.145096	4.329778	45.04932	0.0001140	0.0049161
PLCB2	-3.129927	3.219895	51.74126	0.0000685	0.0037557
AIF1L	-3.108962	6.167169	83.38509	0.0000111	0.0016097
ITGB1BP2	-3.103756	5.368974	86.36585	0.0000097	0.0015449
PPP1R1C	-3.100553	3.392007	44.24209	0.0001217	0.0051481
FGF13-AS1	-3.097264	1.849855	30.03096	0.0040713	0.0379895
SLC5A12	-3.096242	2.155342	42.05370	0.0006515	0.0129466
NPPA	-3.091703	12.905503	43.44037	0.0001301	0.0053098
CDCA3	-3.086259	3.713057	43.92216	0.0001250	0.0052069
GABRA4	-3.068427	3.055071	56.75777	0.0000485	0.0031436
CAV3	-3.066379	3.136842	54.16213	0.0000578	0.0034176
KIF20A	-3.066232	4.724288	37.42469	0.0002218	0.0073503
SELENOP	-3.060758	6.162977	101.98209	0.0000045	0.0012883
CRYM	-3.048275	3.285350	63.43901	0.0000319	0.0027505
DHFR	-3.035134	4.171379	97.32632	0.0000052	0.0013682
BBOX1-AS1	-3.034916	1.824077	29.38297	0.0052955	0.0449764
ZWINT	-3.030731	4.480563	108.41300	0.0000034	0.0012869
SPC24	-3.025167	2.311906	38.16759	0.0002206	0.0073354
COL9A1	-3.024658	2.758275	46.92348	0.0000982	0.0045464
PANCR	-3.015240	1.815120	14.93628	0.0055620	0.0463645
NUDT7	-3.015061	3.352483	53.07165	0.0000624	0.0035579
C1orf105	-3.013779	4.009494	32.81289	0.0003512	0.0094029
HOPX	-3.009609	7.911857	53.76810	0.0000594	0.0034598
TOP2A	-3.004569	5.879015	28.96886	0.0005376	0.0116181
FRMD3	-2.990653	5.739911	93.15264	0.0000067	0.0014750
G0S2	-2.979050	7.268480	56.38213	0.0000498	0.0031761
LINC01405	-2.969873	2.961599	26.87404	0.0006912	0.0134324
AQP10	-2.967106	3.608513	79.67574	0.0000124	0.0017273
PTGES3L	-2.953571	4.445324	71.78529	0.0000199	0.0022436
SGO1	-2.953492	2.308654	44.24394	0.0002917	0.0085806
NEIL3	-2.948272	2.142895	30.75930	0.0009914	0.0163900
HRC	-2.948080	5.050080	67.43540	0.0000253	0.0025180
UBE2T	-2.922022	5.089443	52.70717	0.0000640	0.0036260
RXRG	-2.913305	2.757656	58.02664	0.0000435	0.0030255
NREP	-2.911058	9.793089	100.85041	0.0000045	0.0012883
MCM5	-2.908502	4.683402	83.03824	0.0000108	0.0016057
C11orf52	-2.904686	1.917112	31.22355	0.0040481	0.0378087
CSRP3	-2.882775	10.273352	52.55780	0.0000647	0.0036353
LEFTY2	-2.880727	6.331081	85.03661	0.0000098	0.0015449
LGALS3	-2.871758	6.964936	44.40718	0.0001201	0.0051121
VSTM2L	-2.866543	4.189090	83.29184	0.0000103	0.0015856
CRIP1	-2.865284	2.788855	15.70018	0.0036869	0.0358349
KIF2C	-2.860460	3.511325	37.99659	0.0002102	0.0071578
ENPP5	-2.856968	2.969325	62.31754	0.0000331	0.0027908
NCAPH	-2.854564	2.669372	48.09446	0.0000897	0.0043060
LINC01456	-2.832459	2.159370	22.93684	0.0011594	0.0178687
FMC1	-2.830633	3.939974	14.24424	0.0048637	0.0425396
HMGB2	-2.830279	6.353012	70.47858	0.0000213	0.0023028
IMMP1L	-2.829254	3.758604	27.23721	0.0006610	0.0130629
EMC10	-2.824767	7.218908	53.96630	0.0000586	0.0034433
RAB9B	-2.823723	5.225387	84.33594	0.0000098	0.0015449
TNNT2	-2.820532	11.602913	85.74207	0.0000086	0.0015265
ASF1B	-2.817701	3.439544	58.59071	0.0000431	0.0030190
SLC38A3	-2.806756	2.273880	56.91351	0.0006085	0.0124300
SLC15A2	-2.804699	3.817950	18.75361	0.0021757	0.0260484
SRPK3	-2.800609	2.518381	55.37483	0.0000997	0.0045547
SMIM1	-2.796013	2.308004	20.64358	0.0016181	0.0217183
H4C3	-2.794520	6.630227	31.07645	0.0004235	0.0103480
CSPG5	-2.786076	3.521300	34.54088	0.0002939	0.0086206
MOG	-2.766072	4.236609	84.58887	0.0000092	0.0015377
SH3BGR	-2.764689	7.778034	64.79127	0.0000294	0.0026381
REC114	-2.761811	1.908698	38.33366	0.0057718	0.0472623
FPGT-TNNI3K	-2.753526	4.400054	45.86065	0.0001068	0.0047481
EPN3	-2.749571	2.721405	37.55292	0.0002191	0.0073154
PIMREG	-2.749342	3.111311	29.93996	0.0004808	0.0110608
NMRK2	-2.747681	3.532615	34.16588	0.0003053	0.0087842
TRDN	-2.737878	7.398021	49.95256	0.0000781	0.0039752
POLE2	-2.734335	2.297587	44.12856	0.0006263	0.0126560
CDC45	-2.726066	2.708403	75.86047	0.0000294	0.0026381
DIRAS3	-2.722534	5.246650	76.62062	0.0000147	0.0019306
AMT	-2.719618	4.128716	81.19617	0.0000109	0.0016057
SPX	-2.708569	3.364626	45.78802	0.0001074	0.0047481
CEP55	-2.708550	3.253160	49.05146	0.0000835	0.0041158
CDCA8	-2.698342	2.891869	74.74704	0.0000149	0.0019306
PEBP4	-2.695043	2.159622	27.51015	0.0016200	0.0217289
HRH2	-2.694184	4.686904	80.59530	0.0000115	0.0016253
LINC00881	-2.692807	6.336775	48.43943	0.0000874	0.0042358
SORCS3	-2.687721	2.202008	16.34044	0.0032823	0.0334246
SMYD1	-2.687409	8.634806	28.36640	0.0005770	0.0120621
GPR22	-2.683250	5.043313	53.23310	0.0000617	0.0035385
SYNPO2L	-2.672782	7.679458	109.86419	0.0000032	0.0012769
IGSF5	-2.672417	1.938644	22.12059	0.0058814	0.0477494
SPHKAP	-2.668391	4.785341	15.14208	0.0040910	0.0380828
ANLN	-2.662587	6.618821	17.22171	0.0028113	0.0304452
CAVIN3	-2.661827	4.205267	34.28699	0.0003016	0.0087394
CASQ2	-2.660241	7.989766	60.47205	0.0000382	0.0029093
PLAC1	-2.658369	2.116653	36.02356	0.0023151	0.0270255
MYZAP	-2.654654	7.178472	60.03675	0.0000393	0.0029433
GPX3	-2.652738	7.094667	68.89002	0.0000232	0.0023965
SGCA	-2.644098	4.754303	41.16441	0.0001579	0.0060764
DTL	-2.641167	3.591869	30.23422	0.0004651	0.0109002
SLC27A6	-2.640879	6.575514	54.23099	0.0000575	0.0034118
PDE1A	-2.636327	3.385269	23.96150	0.0010071	0.0165225
UBE2E1	-2.633303	4.594498	69.68775	0.0000218	0.0023298
TYRP1	-2.631008	2.466986	40.73282	0.0002766	0.0083233
MLIP	-2.626909	7.348806	84.30360	0.0000092	0.0015377
TMEM71	-2.625232	4.413872	97.84239	0.0000051	0.0013501
C11orf71	-2.622072	3.166488	38.02702	0.0002096	0.0071578
NDUFB1	-2.617046	6.337492	30.04038	0.0004754	0.0110002
CASQ1	-2.614019	4.993688	68.94170	0.0000227	0.0023790
BIRC5	-2.603424	5.104400	93.38285	0.0000061	0.0014197
TMEM163	-2.592041	3.422335	50.45680	0.0000752	0.0039232
BRINP2	-2.587693	2.272114	19.14654	0.0020422	0.0249842
RRM2	-2.581340	4.726851	85.00166	0.0000089	0.0015377
SFRP5	-2.580538	6.389999	94.15028	0.0000059	0.0014197
GPR183	-2.580100	3.926360	50.07615	0.0000774	0.0039749
PKMYT1	-2.575518	2.462613	23.35632	0.0010938	0.0173235
ALDOC	-2.573856	7.391990	80.38366	0.0000112	0.0016097
PKIA	-2.570428	6.340182	81.60448	0.0000105	0.0015867
MIR1-1HG-AS1	-2.567849	3.616688	36.81472	0.0002350	0.0075473
CRABP2	-2.565913	9.841161	55.27158	0.0000533	0.0032771
SLC26A9	-2.565358	3.137698	30.38541	0.0004572	0.0108234
NEK2	-2.561090	3.131411	65.36739	0.0000254	0.0025192
TYMSOS	-2.551361	2.217243	17.47788	0.0026904	0.0297094
RMI2	-2.542336	3.494177	61.93021	0.0000336	0.0028119
FERMT1	-2.540029	3.767847	40.69317	0.0001646	0.0061634
COX7C	-2.538748	8.321217	29.86352	0.0004850	0.0111182
DEPDC1	-2.538447	4.163804	87.00594	0.0000081	0.0015101
CKAP2L	-2.533517	3.063747	70.12482	0.0000191	0.0021905
PNMT	-2.532905	2.044650	19.91435	0.0046481	0.0413085
MINCR	-2.531948	2.317575	14.95233	0.0042409	0.0388960
CDK1	-2.528634	4.720155	87.35193	0.0000080	0.0015101
C11orf1	-2.523570	3.699331	26.42569	0.0007309	0.0138976
UPK1B	-2.518697	3.740335	57.65215	0.0000458	0.0030761
SMIM5	-2.507403	2.351641	28.80567	0.0008846	0.0153204
GIHCG	-2.502606	4.070940	29.06195	0.0005318	0.0115694
CCNB2	-2.500282	3.957803	72.93954	0.0000164	0.0019783
APOBEC2	-2.495307	6.768766	62.32141	0.0000341	0.0028119
ZNF793-AS1	-2.482754	2.441286	21.09526	0.0015121	0.0210436
ADHFE1	-2.470553	4.039047	86.42228	0.0000084	0.0015101
RPE65	-2.467311	2.822103	66.21730	0.0000409	0.0029867
PHACTR3	-2.466546	2.039413	27.35219	0.0057898	0.0473388
PRADC1	-2.464355	5.446662	35.51929	0.0002665	0.0081854
ACOT2	-2.463990	5.114293	49.12256	0.0000830	0.0041098
MTERF2	-2.454024	5.093586	67.08827	0.0000241	0.0024364
HJURP	-2.451450	3.224890	26.36827	0.0007362	0.0139381
TSTD1	-2.443933	4.921833	25.47405	0.0008248	0.0147548
DUSP27	-2.443680	6.220475	13.41977	0.0057387	0.0471570
CLYBL	-2.443256	2.658529	66.05325	0.0001572	0.0060712
SFRP2	-2.438680	3.032048	47.78984	0.0000919	0.0043544
LRRCC1	-2.437214	2.813535	51.67542	0.0000641	0.0036260
IDNK	-2.433926	2.567916	29.80141	0.0004884	0.0111607
LINC02384	-2.433270	2.453138	22.62358	0.0012116	0.0183854
EXOC3-AS1	-2.430176	2.912271	24.60638	0.0009239	0.0157850
PHOSPHO2	-2.427786	2.270983	20.61858	0.0018242	0.0233347
KCNS2	-2.425896	2.613848	14.64476	0.0044984	0.0403073
GSG1	-2.424480	3.188673	36.02896	0.0002535	0.0079002
NUSAP1	-2.423946	4.639302	54.63118	0.0000560	0.0033764
LRRC10	-2.418899	6.726833	76.60740	0.0000135	0.0018385
TMEM141	-2.417552	5.353739	40.87874	0.0001619	0.0061221
NEBL	-2.413640	8.496396	62.65125	0.0000305	0.0026939
NES	-2.412128	6.009236	83.62319	0.0000095	0.0015449
TRAPPC6A	-2.409063	4.164939	26.67639	0.0007084	0.0136149
SLC8A1	-2.406968	7.232354	21.61727	0.0014000	0.0200824
CENPH	-2.395725	3.282142	26.98076	0.0006822	0.0132934
PHYHD1	-2.395036	3.490711	22.24569	0.0012784	0.0189503
SLC30A3	-2.395008	3.500846	73.30616	0.0000160	0.0019774
C11orf74	-2.390511	5.097256	43.62940	0.0001280	0.0052897
RCSD1	-2.389719	5.725755	40.11165	0.0001733	0.0064524
C14orf180	-2.386624	3.731630	83.44604	0.0000096	0.0015449
HSPB1	-2.385072	9.805323	28.48780	0.0005688	0.0119630
EPHX2	-2.384289	3.277717	58.93125	0.0000384	0.0029093
VIPR1	-2.382483	2.895056	26.39228	0.0007340	0.0139155
NTF4	-2.377098	2.412150	39.50176	0.0009882	0.0163644
RPA3	-2.365246	4.819416	23.48409	0.0010748	0.0171617
FN3K	-2.364778	2.901139	31.40227	0.0004086	0.0101674
MRPS28	-2.358498	4.865356	35.90387	0.0002567	0.0079818
ZSCAN16-AS1	-2.356234	2.830133	18.93723	0.0021120	0.0254701
TAGLN3	-2.354777	2.218534	23.67249	0.0030785	0.0321670
UBE2C	-2.349332	4.367176	29.13546	0.0005273	0.0115222
DNAAF3	-2.348180	2.676828	34.24139	0.0003030	0.0087394
HSD17B8	-2.345639	2.959449	31.66687	0.0003970	0.0100521
CRYAB	-2.344243	8.985251	28.13487	0.0005931	0.0122128
TRDN-AS1	-2.340617	4.534752	58.23960	0.0000430	0.0030190
FOXM1	-2.340321	3.451918	17.45867	0.0026992	0.0297234
C17orf97	-2.335326	2.570693	50.28160	0.0004459	0.0106832
PDE6B	-2.333192	3.174401	55.87002	0.0000476	0.0031122
CLIC5	-2.332800	6.040528	28.35788	0.0005776	0.0120621
TMOD1	-2.329743	7.113926	72.72280	0.0000166	0.0019783
FPGT	-2.329109	2.490108	40.10933	0.0008135	0.0146726
LINC01778	-2.327603	2.512025	22.71131	0.0011967	0.0182601
LRRC52-AS1	-2.324422	3.644391	28.82426	0.0005467	0.0116920
CDCA5	-2.322462	2.828126	58.95710	0.0000791	0.0039997
TK1	-2.320187	4.733006	44.87929	0.0001156	0.0049515
MORN2	-2.319151	4.207714	23.49178	0.0010736	0.0171617
GP1BB	-2.314509	2.952443	15.63393	0.0037322	0.0360061
ATP5PF	-2.312218	8.040040	26.06763	0.0007646	0.0142109
COL21A1	-2.309664	4.739278	60.83793	0.0000352	0.0028119
DRD1	-2.305130	2.545329	14.66026	0.0044850	0.0402249
ACSM5	-2.303018	2.385382	53.88208	0.0015739	0.0214354
NDUFA3	-2.302154	6.004117	19.42939	0.0019524	0.0243560
BOLA1	-2.296717	3.132734	18.12030	0.0024143	0.0277539
CCND2-AS1	-2.295584	2.929593	16.76507	0.0030441	0.0319432
BIK	-2.292042	4.562095	23.07729	0.0011369	0.0177094
CORO6	-2.289832	6.372772	66.69967	0.0000232	0.0023965
S100A6	-2.287949	4.171578	18.35223	0.0023233	0.0270728
HAND1	-2.281999	4.021494	50.06068	0.0000774	0.0039749
KIAA0319	-2.281731	2.523846	13.55462	0.0055830	0.0464215
COX7B	-2.281664	7.853033	24.18374	0.0009774	0.0162955
CRIP2	-2.272728	9.555222	34.10054	0.0003073	0.0088094
CAMK2A	-2.271184	2.230374	45.24312	0.0039582	0.0372525
TECRL	-2.264283	7.866569	48.02889	0.0000902	0.0043066
ACOT1	-2.259996	2.526954	43.28432	0.0007880	0.0143980
HAND2	-2.255680	5.989330	42.70144	0.0001384	0.0055198
DERL3	-2.255450	2.906581	31.94353	0.0003853	0.0098337
BANCR	-2.253846	6.871978	31.61210	0.0003994	0.0100730
NIPSNAP3B	-2.253375	3.162935	39.37680	0.0001851	0.0067394
LYRM9	-2.250067	2.882413	33.06088	0.0003422	0.0093395
SRP14-AS1	-2.245190	3.680198	36.17603	0.0002499	0.0078599
BCL2A1	-2.242443	2.254108	14.98819	0.0042120	0.0387554
UNC45B	-2.241744	8.454851	18.61016	0.0022271	0.0264539
CTF1	-2.240603	3.827212	30.40420	0.0004563	0.0108137
ANKRD1	-2.238789	9.282733	24.45587	0.0009425	0.0159288
KIF22	-2.232446	4.345682	70.54815	0.0000186	0.0021763
YPEL1	-2.232118	4.170625	67.48255	0.0000222	0.0023479
LYPD6	-2.228899	2.397693	15.38210	0.0039108	0.0369840
TBX20	-2.225745	3.898102	56.62588	0.0000455	0.0030701
SCHIP1	-2.222649	5.878322	71.90855	0.0000173	0.0020453
SLC2A8	-2.222631	4.835923	57.00676	0.0000451	0.0030518
PLK4	-2.221475	2.626243	16.41406	0.0032394	0.0331622
SYNJ2BP-COX16	-2.221443	3.773208	32.91179	0.0003476	0.0093542
CDC6	-2.216078	3.672923	21.20415	0.0014878	0.0208241
KCNQ2	-2.214763	3.048884	26.12628	0.0007590	0.0141490
GON7	-2.209077	3.519188	23.17055	0.0011223	0.0175621
ACAT1	-2.204879	6.880535	69.95317	0.0000193	0.0021988
VSNL1	-2.201836	4.885539	56.22627	0.0000475	0.0031122
CDC20	-2.200800	3.810945	61.78922	0.0000312	0.0027335
ACADSB	-2.198825	4.134325	16.78102	0.0030355	0.0318708
SELENOW	-2.198793	9.304079	29.34283	0.0005148	0.0113764
LINC00526	-2.197931	2.732049	16.93661	0.0029539	0.0312987
COX6C	-2.195835	8.360781	23.13352	0.0011281	0.0176244
REXO5	-2.195596	3.426408	20.84830	0.0015689	0.0214354
SSPN	-2.183134	4.659579	27.07836	0.0006740	0.0131871
DAND5	-2.181966	2.602316	24.45002	0.0009432	0.0159288
RBMS3-AS3	-2.180075	2.357659	22.80648	0.0026288	0.0293933
HMGCLL1	-2.178475	3.329774	63.32700	0.0000284	0.0026266
LINC00880	-2.177140	4.941708	58.97843	0.0000377	0.0029093
C10orf71	-2.176344	2.517078	13.39051	0.0057732	0.0472623
HMGN2	-2.174406	7.534315	37.74387	0.0002152	0.0072678
MYL9	-2.170793	9.804863	43.82020	0.0001213	0.0051481
ROGDI	-2.167941	5.631528	44.24487	0.0001217	0.0051481
PLN	-2.167092	10.586009	32.98622	0.0003449	0.0093542
HAND2-AS1	-2.167011	5.831762	64.36575	0.0000266	0.0025505
PCBD1	-2.167003	5.394227	27.40924	0.0006473	0.0128954
MPC1	-2.165892	6.005173	24.23629	0.0009706	0.0162227
TAFA2	-2.164442	2.255294	24.39671	0.0050199	0.0433758
DNAJC28	-2.164137	2.445701	24.11364	0.0017714	0.0228985
INKA2	-2.162963	4.047909	45.79497	0.0001074	0.0047481
USH1C	-2.162887	2.287685	20.73651	0.0042933	0.0391865
NDUFS6	-2.162245	6.404731	29.01831	0.0005345	0.0115897
ADCY5	-2.158902	6.403468	18.51693	0.0022613	0.0265902
MDP1	-2.154549	4.111410	26.29860	0.0007426	0.0139891
PMEL	-2.153426	3.412220	49.85708	0.0000736	0.0038614
MTURN	-2.152774	4.617683	56.33443	0.0000460	0.0030777
LINC01351	-2.148929	2.241988	28.24087	0.0052656	0.0448276
LINC02762	-2.143704	4.734591	28.17354	0.0005904	0.0121937
ULK4	-2.138354	3.556534	52.49176	0.0000597	0.0034670
DLGAP1-AS1	-2.134387	2.569413	15.58070	0.0037691	0.0361948
DES	-2.134094	7.311249	53.44978	0.0000559	0.0033764
TMEM97	-2.134051	4.002616	64.21022	0.0000269	0.0025570
SLC5A1	-2.133719	4.807662	18.20450	0.0023808	0.0275223
PRC1	-2.133292	4.849762	29.60058	0.0004998	0.0112467
DECR1	-2.132021	6.754908	53.62447	0.0000559	0.0033764
GLIDR	-2.130896	3.395435	38.39637	0.0002025	0.0070229
HMGN5	-2.130325	2.776836	22.89057	0.0011669	0.0178976
SHCBP1	-2.129381	3.220118	17.35530	0.0027474	0.0300854
ATP5ME	-2.123243	6.673001	20.47854	0.0016591	0.0220280
SYNM	-2.122636	5.032839	14.79312	0.0043718	0.0395976
UQCRQ	-2.122164	8.188141	23.99711	0.0010023	0.0164998
NDUFB2	-2.118844	7.042373	23.87766	0.0010186	0.0166153
CMC4	-2.118674	4.267070	25.08004	0.0008681	0.0151960
ITM2A	-2.118308	3.567860	27.99204	0.0006033	0.0123602
BEX2	-2.111248	4.212815	32.95306	0.0003461	0.0093542
MGST3	-2.109753	8.346264	21.65019	0.0013933	0.0200007
ANAPC16	-2.104280	7.102962	35.44008	0.0002686	0.0082305
MRPL53	-2.101326	5.157360	19.83226	0.0018327	0.0233988
NAP1L3	-2.099201	5.370958	37.98851	0.0002103	0.0071578
IL20RA	-2.099056	2.714177	36.71103	0.0005470	0.0116920
ATP5MC3	-2.098677	8.587440	29.02713	0.0005340	0.0115897
GUCY1A1	-2.098464	8.470145	45.22582	0.0001080	0.0047643
MYBPC3	-2.098119	8.888559	15.80577	0.0036160	0.0353217
CDKN2C	-2.096007	2.806192	27.16126	0.0006672	0.0130934
KLHL3	-2.095120	5.065742	21.68043	0.0013872	0.0199564
EFCAB7	-2.091420	3.359217	50.90181	0.0000656	0.0036581
GTSE1	-2.089318	2.842977	45.09877	0.0002398	0.0076380
ASB2	-2.088868	6.945506	37.00136	0.0002308	0.0075122
EMP2	-2.088006	6.850257	31.32778	0.0004119	0.0101815
GNG7	-2.087833	3.678315	64.54015	0.0000264	0.0025481
DOK7	-2.086878	4.289914	73.31434	0.0000160	0.0019774
PHACTR1	-2.086106	4.967612	49.77250	0.0000759	0.0039278
PLPP7	-2.082147	5.797028	56.29100	0.0000446	0.0030414
FAM229B	-2.080910	5.638910	32.65186	0.0003573	0.0094353
CDCA7	-2.075812	2.507710	19.71112	0.0020206	0.0248592
HIGD2A	-2.075338	6.919949	18.70036	0.0021946	0.0261471
ICA1	-2.073635	4.836517	68.83267	0.0000205	0.0022828
ATP5PD	-2.070352	7.400018	25.90665	0.0007804	0.0143064
PARP1	-2.069997	7.027387	33.84833	0.0003154	0.0088535
TMEM144	-2.068687	3.363263	57.90221	0.0000401	0.0029548
SH3RF2	-2.067586	4.951165	51.65734	0.0000642	0.0036260
DGCR6	-2.064497	4.510378	28.97295	0.0005373	0.0116181
NDUFC1	-2.062849	6.706193	19.79048	0.0018447	0.0234906
ACYP1	-2.061079	3.705755	16.05494	0.0034555	0.0345052
COX8A	-2.061003	7.174523	18.02479	0.0024531	0.0280842
MYLK	-2.060309	9.251826	39.45907	0.0001812	0.0066224
FAM20A	-2.059499	2.536403	23.34206	0.0016766	0.0222278
PLCXD3	-2.058581	4.883096	45.79334	0.0001064	0.0047457
ABHD11	-2.056984	3.790402	36.09377	0.0002519	0.0078889
MMP15	-2.056655	6.566182	23.07605	0.0011371	0.0177094
ST7-AS1	-2.056492	2.512928	37.15366	0.0019371	0.0241803
NSMCE4A	-2.054613	5.063454	55.80641	0.0000461	0.0030777
INKA2-AS1	-2.054012	2.680850	43.39229	0.0007955	0.0144810
NEXN	-2.052929	7.854613	26.66831	0.0007091	0.0136149
ATP5MF	-2.049363	6.800521	20.18405	0.0017356	0.0225697
PPP1R14C	-2.047443	7.214625	47.84907	0.0000868	0.0042247
NIFK-AS1	-2.046841	2.901511	41.10360	0.0002045	0.0070518
ERH	-2.046144	6.396813	26.20089	0.0007518	0.0140776
HACD1	-2.043966	7.480174	26.17384	0.0007544	0.0140989
PET100	-2.043188	5.273546	19.17708	0.0020323	0.0249403
SMDT1	-2.037491	5.542199	24.53255	0.0009330	0.0158372
RDH5	-2.037272	3.028846	23.52853	0.0010683	0.0171617
DNAJC15	-2.036522	4.760353	33.85317	0.0003152	0.0088535
PIFO	-2.030697	3.565426	34.43401	0.0002971	0.0086644
ETFRF1	-2.029499	4.676854	20.12125	0.0017525	0.0226838
SKA3	-2.028284	2.472653	24.59829	0.0028315	0.0305793
GJA5	-2.025339	5.790669	22.33501	0.0012622	0.0188791
DHRS11	-2.024969	2.355453	31.98705	0.0046921	0.0415305
GSTM4	-2.024015	5.693714	36.46172	0.0002431	0.0077321
ATP5MC1	-2.023177	6.647563	21.24909	0.0014779	0.0207022
MYL3	-2.022303	8.201414	31.77318	0.0003925	0.0099627
TIMM8B	-2.021806	5.967973	25.75849	0.0007953	0.0144810
ATP5MPL	-2.020557	7.320474	20.41067	0.0016764	0.0222278
CHCHD5	-2.019536	3.888336	17.55777	0.0026540	0.0295236
IL17B	-2.019427	2.383419	20.90870	0.0041069	0.0381662
PPP1R3C	-2.018053	4.783392	29.60422	0.0004996	0.0112467
SVIP	-2.011910	3.910878	16.67467	0.0030929	0.0322491
HADH	-2.010848	5.595895	68.67077	0.0000207	0.0022838
UQCR10	-2.010785	7.642238	20.76159	0.0015895	0.0215560
CHURC1-FNTB	-2.009534	3.707609	30.17326	0.0004683	0.0109265
FANCL	-2.006840	4.456246	56.40377	0.0000443	0.0030414
CPVL	-2.005104	6.774119	60.13375	0.0000346	0.0028119
PLK1	-2.000453	3.879544	55.08925	0.0000484	0.0031436
ACOT13	-2.000114	5.847783	30.46547	0.0004532	0.0107527
PTBP3	2.004432	5.518912	29.26607	0.0005194	0.0114385
TGFBI	2.008175	8.222606	22.90922	0.0011639	0.0178976
RLF	2.009219	6.916310	24.51223	0.0009355	0.0158515
ERO1A	2.009337	6.150180	39.92083	0.0001763	0.0065139
MYD88	2.019954	5.073590	30.86736	0.0004333	0.0104852
LRIG3	2.022030	4.074215	23.79939	0.0010295	0.0167509
GTF2IRD1	2.022119	5.320018	40.71978	0.0001642	0.0061607
PIM3	2.022238	5.524202	64.94521	0.0000257	0.0025377
RSRC2	2.024864	7.386379	58.53508	0.0000384	0.0029093
PIGA	2.025300	4.525591	33.41666	0.0003297	0.0091468
ARRDC2	2.028687	2.975729	46.06784	0.0001172	0.0050104
CASP4	2.031420	4.582159	45.33682	0.0001110	0.0048176
KCNE4	2.032976	5.291654	43.40793	0.0001304	0.0053098
TLE1	2.036129	5.850678	32.45804	0.0003647	0.0095666
EGR1	2.037634	7.201431	39.15933	0.0001888	0.0068231
HRH1	2.039099	4.520897	66.50932	0.0000235	0.0024106
EVC2	2.040074	3.251847	28.55813	0.0005641	0.0118834
H2BC5	2.042077	3.796569	33.39466	0.0003305	0.0091468
LIPG	2.043150	3.120983	30.06482	0.0004741	0.0110002
EMP1	2.044095	3.812334	38.37499	0.0002029	0.0070229
HAPLN3	2.047483	4.194068	74.36986	0.0000152	0.0019319
PIK3CD	2.048266	3.513463	26.05156	0.0007662	0.0142109
DBP	2.048628	4.124211	59.13743	0.0000369	0.0028841
ADM2	2.052314	3.681901	35.21260	0.0002748	0.0083105
BAIAP2L1	2.054319	3.244316	25.61844	0.0008097	0.0146300
PFKFB3	2.054620	6.220168	15.56250	0.0037818	0.0362354
TRIM22	2.055730	6.297457	25.72451	0.0007987	0.0145127
PDZD2	2.058617	3.287078	41.29298	0.0001562	0.0060442
ZNF844	2.061578	3.110554	21.42606	0.0014398	0.0205036
ITGA2	2.062052	5.779381	36.02532	0.0002536	0.0079002
DOK5	2.067119	4.379998	72.74209	0.0000165	0.0019783
SKIL	2.067251	6.890339	71.06788	0.0000181	0.0021288
PCSK9	2.069441	2.878845	35.17666	0.0002758	0.0083139
RAPGEF2	2.072268	6.336223	37.49660	0.0002202	0.0073354
NPIPB15	2.073422	2.578592	24.83420	0.0011091	0.0174534
CLCF1	2.075358	2.714797	34.93737	0.0004695	0.0109413
RGS16	2.075771	2.246447	14.59476	0.0056342	0.0465904
ADCY7	2.076348	3.765286	32.91226	0.0003476	0.0093542
KLF9	2.079559	2.831800	31.39751	0.0004088	0.0101674
SQSTM1	2.082316	10.098863	57.79548	0.0000403	0.0029646
FGF7	2.083364	5.050689	46.79790	0.0000988	0.0045511
SH3RF1	2.084813	6.094909	27.20199	0.0006639	0.0130802
CDH6	2.086026	3.842225	55.08953	0.0000487	0.0031438
HOXA-AS2	2.088457	3.095199	35.63492	0.0002635	0.0081436
NBPF14	2.093447	5.379842	64.62730	0.0000262	0.0025480
UBASH3B	2.093595	3.201016	39.89774	0.0001766	0.0065151
ZNF317	2.095386	6.258907	18.24073	0.0023665	0.0274296
IFRD1	2.095692	6.835812	61.33781	0.0000321	0.0027505
PDE7A	2.096324	5.599562	37.26773	0.0002251	0.0074103
TMEM87B	2.099924	5.543321	38.74301	0.0001961	0.0069235
DPP4	2.104114	3.978669	21.26956	0.0014735	0.0207016
C1QTNF1	2.109298	4.248291	43.41985	0.0001303	0.0053098
MVP	2.111094	6.994655	42.08814	0.0001458	0.0056996
ERRFI1	2.113944	7.003143	24.13875	0.0009833	0.0163127
KLF11	2.114600	5.413462	17.94407	0.0024864	0.0283832
NRG3	2.120995	3.509814	54.36167	0.0000514	0.0032300
SLC38A5	2.122949	2.645344	36.38028	0.0005832	0.0120940
ARHGAP20	2.123484	2.634645	24.11675	0.0009863	0.0163457
THSD1	2.128001	2.363420	20.24808	0.0027872	0.0302996
IL33	2.129479	5.178257	68.35190	0.0000211	0.0022998
TENT5C	2.132303	3.190938	24.57125	0.0009282	0.0158242
RXFP1	2.133374	2.598005	17.13141	0.0028556	0.0307207
NBPF26	2.135125	5.269142	26.29526	0.0007430	0.0139891
THY1	2.139841	7.881571	48.91955	0.0000806	0.0040457
TYMP	2.142315	3.825328	27.48119	0.0006417	0.0128615
GBP3	2.142594	4.570524	26.94510	0.0006852	0.0133387
STARD13	2.146103	5.337618	26.34210	0.0007386	0.0139479
LDB2	2.155333	4.882540	55.32438	0.0000501	0.0031761
EIF2AK2	2.155542	6.387405	27.20722	0.0006635	0.0130802
HS6ST2	2.158807	2.247820	20.55080	0.0043804	0.0395997
ZBTB10	2.166943	5.196433	23.02788	0.0011448	0.0177862
CHD1	2.167425	6.450497	49.55368	0.0000799	0.0040307
GADD45B	2.169566	7.554465	59.97477	0.0000350	0.0028119
NFKBID	2.170539	2.547989	52.98504	0.0008309	0.0148364
SEC24A	2.171192	6.533926	13.53523	0.0056050	0.0465458
HFE	2.173138	2.553298	44.69194	0.0008030	0.0145489
KCNAB1	2.174609	3.216456	68.84353	0.0000205	0.0022828
SEL1L3	2.178554	6.491276	17.09245	0.0028749	0.0308611
LRRC8E	2.181391	2.746993	21.81094	0.0013611	0.0197421
PTGIS	2.183773	8.541022	45.82255	0.0001059	0.0047334
ACHE	2.184265	4.274795	76.04896	0.0000139	0.0018792
NEDD9	2.198391	7.346351	22.41278	0.0012483	0.0187707
TBC1D2	2.199856	2.787065	31.87433	0.0003882	0.0098882
IL1RL1	2.200511	7.940512	39.48969	0.0001832	0.0066833
ATP8B1	2.201638	4.908575	24.29311	0.0009632	0.0161408
SMURF1	2.206765	6.367100	14.95457	0.0042391	0.0388960
CACTIN	2.216597	5.371437	35.65443	0.0002630	0.0081408
WAKMAR2	2.221539	2.255501	35.50517	0.0033638	0.0340250
GPBP1	2.221672	7.846399	45.51049	0.0001098	0.0048017
SNAPC1	2.224079	6.031346	74.62952	0.0000150	0.0019306
CLK4	2.230614	5.934948	46.22436	0.0001038	0.0046814
MFAP3L	2.230693	3.271002	25.00516	0.0008766	0.0152898
SPRED3	2.232555	2.258711	31.46815	0.0032174	0.0330170
FOXN2	2.235189	4.821019	38.30894	0.0002041	0.0070518
SMOX	2.238389	4.386918	63.07335	0.0000291	0.0026381
DTX3L	2.238600	4.502182	39.29451	0.0001865	0.0067647
TNFAIP2	2.246920	2.435379	31.99143	0.0011633	0.0178976
DUSP6	2.247526	6.615571	59.10035	0.0000387	0.0029093
ETV4	2.255293	3.389742	51.16339	0.0000698	0.0037609
DRAM1	2.255817	5.547865	49.94757	0.0000781	0.0039752
RASGRF2	2.257768	3.281691	27.15870	0.0006674	0.0130934
ARSI	2.258777	3.445717	57.34857	0.0000428	0.0030190
SLC7A5	2.268056	8.820527	25.50067	0.0008220	0.0147311
SPRED1	2.268266	5.631474	32.44575	0.0003652	0.0095666
STEAP1	2.269506	2.158776	34.45582	0.0046983	0.0415667
HES1	2.272304	6.315384	48.47497	0.0000872	0.0042349
RBM15	2.273480	4.733079	22.39799	0.0012509	0.0187947
ITGA4	2.280581	7.210732	23.24107	0.0011114	0.0174687
DDIT3	2.282792	6.698829	47.72524	0.0000923	0.0043655
GPR176	2.287500	6.829438	25.25024	0.0008491	0.0150044
BRPF1	2.289519	5.016377	18.25805	0.0023597	0.0273672
SERPINB8	2.291079	4.970055	82.51326	0.0000101	0.0015540
DUSP1	2.292234	8.485314	75.91168	0.0000140	0.0018797
TRIM25	2.294127	4.596770	23.47330	0.0010764	0.0171659
CFB	2.294208	3.185792	21.59213	0.0014052	0.0201416
ALDH1A3	2.304578	5.569875	17.07360	0.0028843	0.0309039
HTR7	2.306582	3.975230	29.33506	0.0005153	0.0113764
SULF1	2.309025	10.514876	14.30185	0.0048089	0.0422406
SLC2A9	2.313958	2.664464	51.53580	0.0002084	0.0071561
TAP1	2.318335	6.931737	27.26981	0.0006584	0.0130241
PDK4	2.321624	4.492490	56.64808	0.0000484	0.0031436
EPHA2	2.323694	7.567711	27.87603	0.0006118	0.0124792
SLC43A3	2.324096	3.546745	51.56179	0.0000694	0.0037609
SLC22A3	2.328724	4.729065	37.98477	0.0002104	0.0071578
IRAK2	2.332145	2.903430	52.71759	0.0000589	0.0034522
TRIM38	2.333957	4.789839	61.01720	0.0000353	0.0028119
INTS6	2.335218	6.513688	36.35409	0.0002457	0.0077752
CD44	2.340378	7.554509	45.66604	0.0001085	0.0047730
ELF3	2.340595	4.964933	84.78612	0.0000090	0.0015377
BCL3	2.352478	5.600504	65.95346	0.0000252	0.0025180
BCAR3	2.356021	5.790211	38.71697	0.0001966	0.0069261
ULBP2	2.358103	3.957069	80.46097	0.0000111	0.0016097
JUN	2.358727	8.861739	32.15737	0.0003766	0.0097804
MCTP2	2.360615	3.508561	32.70630	0.0003552	0.0094353
LSMEM1	2.361432	2.317843	45.62247	0.0015010	0.0209329
AMIGO2	2.368723	8.003288	43.69275	0.0001274	0.0052731
ADAM32	2.376574	2.341232	46.01163	0.0012660	0.0189031
APOL1	2.379876	4.122219	21.56230	0.0014113	0.0201856
IRF1	2.379943	4.992209	87.12418	0.0000081	0.0015101
INHBA	2.383219	8.306131	78.67403	0.0000121	0.0017024
MALL	2.383326	2.659139	41.05437	0.0001594	0.0060992
FRMD6	2.387872	6.891291	14.68130	0.0044669	0.0401342
RGS4	2.388592	7.191836	57.83783	0.0000446	0.0030414
CIART	2.392362	4.790032	92.17636	0.0000065	0.0014424
CREBRF	2.394751	6.655744	61.63792	0.0000343	0.0028119
HLA-E	2.405630	7.998819	48.34451	0.0000881	0.0042472
TPBG	2.407003	6.893303	69.75091	0.0000198	0.0022405
TG	2.407486	3.313804	64.08243	0.0000274	0.0025570
TNFRSF1B	2.408509	2.494308	40.14760	0.0004310	0.0104419
CXCL6	2.410656	2.592254	46.90449	0.0002179	0.0073154
TET3	2.410728	4.493949	52.52010	0.0000648	0.0036353
NR6A1	2.414602	2.865905	52.70812	0.0000604	0.0034872
MYO3A	2.414730	2.342404	33.47029	0.0011067	0.0174366
PARP9	2.414755	5.806204	16.66523	0.0030981	0.0322639
BCL6	2.422277	6.040827	70.56460	0.0000190	0.0021905
INSYN2B	2.430209	2.488640	42.73621	0.0004134	0.0101815
NBPF19	2.433163	3.774509	53.83972	0.0000591	0.0034529
LOXL2	2.435605	9.183272	31.59394	0.0004002	0.0100799
HIVEP1	2.437602	6.216610	37.05956	0.0002296	0.0075043
MAPK13	2.450262	2.028206	22.03778	0.0055114	0.0462644
NEFM	2.456494	2.322909	25.11623	0.0010629	0.0171617
SOX17	2.458071	2.337055	58.62437	0.0009577	0.0161040
DUSP4	2.462814	3.126499	58.04295	0.0000427	0.0030190
SLCO2A1	2.466396	2.839009	37.82173	0.0002136	0.0072524
CA12	2.469995	4.680373	66.11578	0.0000262	0.0025480
PDE10A	2.477695	5.789936	54.34658	0.0000571	0.0033950
KLF4	2.478537	2.201813	47.66737	0.0019818	0.0245703
PTGER4	2.483473	2.339761	35.38493	0.0008789	0.0152928
IL15RA	2.483720	2.576531	27.93078	0.0006078	0.0124300
KLF5	2.485018	5.690175	73.25404	0.0000166	0.0019783
BHLHE40	2.496503	7.578998	58.09862	0.0000445	0.0030414
EDEM1	2.498534	5.605145	25.98581	0.0007726	0.0142520
MEDAG	2.503234	3.778340	64.17896	0.0000292	0.0026381
TIGD3	2.508575	2.188260	32.33343	0.0019804	0.0245703
SLC2A3	2.509515	7.984835	31.98997	0.0003834	0.0098214
FNIP2	2.511309	7.557486	28.91908	0.0005407	0.0116472
LOXL3	2.511423	3.727307	62.42745	0.0000329	0.0027841
TRAF1	2.514945	3.056460	53.39919	0.0000610	0.0035080
KLF10	2.515128	7.427442	50.13561	0.0000770	0.0039749
UGCG	2.518274	7.585201	83.56366	0.0000096	0.0015449
VEGFC	2.535167	4.635154	94.71748	0.0000058	0.0014052
CPM	2.545456	3.022765	67.41990	0.0000223	0.0023479
PHLDA2	2.549979	5.303923	43.22775	0.0001324	0.0053487
OVGP1	2.567849	2.209877	35.06004	0.0014456	0.0205290
SPINT1	2.569089	2.654571	59.90095	0.0000670	0.0037034
APOL6	2.571367	3.725652	28.88805	0.0005427	0.0116535
STC2	2.574370	8.153217	47.92961	0.0000909	0.0043208
CSF1	2.579403	6.467006	103.92047	0.0000040	0.0012869
ADIRF-AS1	2.579661	2.075189	18.68391	0.0030687	0.0321160
F2RL1	2.589487	4.255967	53.54420	0.0000603	0.0034872
CD101	2.589927	2.004320	17.59860	0.0043811	0.0395997
HERC6	2.604753	5.322727	13.54169	0.0055977	0.0465044
IL1R1	2.605356	7.513133	24.61197	0.0009232	0.0157850
TNFSF9	2.605547	3.160242	47.56645	0.0000935	0.0044085
GRB7	2.610120	2.239059	26.62211	0.0010549	0.0170510
BMPR1B	2.619521	2.968540	62.37361	0.0000318	0.0027505
TNFRSF10D	2.620613	7.480225	14.94479	0.0042470	0.0389248
HOXA5	2.628181	3.550076	65.55187	0.0000275	0.0025578
PMAIP1	2.637589	5.368933	70.49822	0.0000210	0.0022998
TMED7-TICAM2	2.639298	4.595094	49.37553	0.0000815	0.0040633
PARP14	2.642709	6.036682	14.89076	0.0042909	0.0391865
H2BC8	2.643823	2.446299	49.98735	0.0002391	0.0076380
SGK1	2.647606	8.446304	81.45867	0.0000106	0.0015867
SBNO2	2.656249	4.523733	36.87898	0.0002336	0.0075257
PDCD1LG2	2.657190	3.062061	37.68423	0.0002164	0.0072960
ITGA5	2.665103	9.258279	24.97348	0.0008803	0.0152928
KCNN1	2.667134	2.217189	49.10990	0.0010080	0.0165225
SELPLG	2.668810	3.424445	50.72737	0.0000737	0.0038614
SP100	2.676217	6.869313	49.92929	0.0000782	0.0039752
SERPINB2	2.677729	2.534626	32.68863	0.0003559	0.0094353
GABRR2	2.682761	2.202704	29.53987	0.0010748	0.0171617
WNK4	2.682955	3.808848	82.80079	0.0000099	0.0015449
TM4SF1	2.691544	5.916868	102.61484	0.0000042	0.0012883
BMP6	2.691649	5.361842	39.69598	0.0001799	0.0065847
CCL2	2.692769	7.847590	52.45024	0.0000652	0.0036429
CHD2	2.697284	7.759830	61.58868	0.0000357	0.0028350
ADGRE5	2.699674	4.148737	62.43113	0.0000339	0.0028119
INHBE	2.700693	3.138498	27.32567	0.0006539	0.0129541
ZBTB21	2.703003	4.756237	52.63773	0.0000643	0.0036260
CPA4	2.708803	8.661667	57.24498	0.0000470	0.0031122
H2BC18	2.711889	1.912383	47.22384	0.0053097	0.0450662
SLC19A2	2.718296	4.679205	69.11184	0.0000230	0.0023965
PLOD2	2.720926	9.054149	33.04360	0.0003428	0.0093435
PRR5L	2.722209	2.279041	41.67201	0.0005820	0.0120858
BHLHE41	2.722265	5.510344	79.09856	0.0000128	0.0017608
PTGES	2.722689	4.499698	47.92230	0.0000909	0.0043208
IP6K3	2.727148	3.257753	58.45228	0.0000435	0.0030255
JUNB	2.744661	8.839775	69.48414	0.0000218	0.0023298
RBM47	2.744715	2.345884	34.59026	0.0003440	0.0093542
CCNL1	2.752683	7.774751	110.61420	0.0000031	0.0012769
ARHGEF28	2.759261	2.802980	47.49817	0.0000940	0.0044212
GALNT12	2.762916	4.193289	63.99295	0.0000309	0.0027158
RFLNA	2.764764	4.147928	84.39458	0.0000095	0.0015449
SPHK1	2.772888	6.222188	123.11496	0.0000020	0.0010944
PER1	2.773211	6.060084	87.44212	0.0000083	0.0015101
FOSL1	2.786567	3.793474	112.58099	0.0000029	0.0012769
TMEM200A	2.789991	6.447756	89.28898	0.0000075	0.0015101
KCNG1	2.794918	5.266295	87.31263	0.0000083	0.0015101
APOL3	2.797154	2.342614	21.18435	0.0014922	0.0208704
ARRDC3	2.797668	6.423077	42.94122	0.0001356	0.0054314
CDC14A	2.798065	4.378705	46.86708	0.0000987	0.0045511
SLC5A3	2.807390	6.175750	45.49239	0.0001100	0.0048017
GPR87	2.819893	2.113681	45.56112	0.0012731	0.0189112
HAP1	2.828557	1.875954	17.09753	0.0050469	0.0435322
ATF3	2.834749	6.181991	106.16959	0.0000037	0.0012869
LOX	2.837510	10.821083	42.10166	0.0001456	0.0056996
ICAM1	2.844774	5.364546	70.47057	0.0000214	0.0023028
ANXA10	2.847749	1.829139	51.94006	0.0062174	0.0495546
H2BC6	2.848198	1.878000	30.25758	0.0047705	0.0419783
SAMD9L	2.854908	3.920715	16.87209	0.0029874	0.0315855
ATP10A	2.857127	4.766572	49.82133	0.0000788	0.0039967
PTGS1	2.871569	4.109720	40.56185	0.0001665	0.0062233
PPP1R15A	2.888216	8.511152	94.88975	0.0000058	0.0014052
FAM83G	2.890823	4.646828	39.07453	0.0001903	0.0068633
IFIT1	2.897333	7.041470	17.89687	0.0025062	0.0285093
TMEM158	2.907377	4.242491	89.36416	0.0000077	0.0015101
IPMK	2.909372	3.921477	59.40324	0.0000409	0.0029867
TMEM119	2.916719	2.770240	42.17314	0.0001448	0.0056924
FOS	2.924209	8.202713	111.89453	0.0000030	0.0012769
GCH1	2.930393	3.821751	40.90273	0.0001616	0.0061210
ADCY10	2.934266	2.007223	19.27309	0.0020014	0.0246730
AGTR1	2.936738	1.985556	31.28869	0.0020865	0.0253049
ZSWIM4	2.947280	3.828771	35.24651	0.0002738	0.0083105
SLC20A1	2.959516	8.545497	43.95958	0.0001246	0.0052069
OSMR	2.968027	6.966265	28.35249	0.0005780	0.0120621
LINC01119	2.971468	2.172242	58.56300	0.0005557	0.0118139
TNFRSF6B	2.973553	2.364744	31.54205	0.0004024	0.0100851
TLR4	2.977475	4.828423	42.32298	0.0001429	0.0056540
NPIPB6	2.977480	3.411860	58.29854	0.0000439	0.0030414
IL6	2.982850	4.006756	88.50850	0.0000082	0.0015101
TMEM255B	2.982863	3.190498	86.45227	0.0000084	0.0015101
APLN	2.991301	1.846589	47.13043	0.0042620	0.0390111
ADM5	2.995367	1.815252	39.98235	0.0050671	0.0436486
PFKFB4	2.996145	4.417500	61.31929	0.0000363	0.0028708
EGR2	2.997124	4.464698	91.86878	0.0000071	0.0015101
FNDC11	3.003023	2.063081	24.45838	0.0010925	0.0173168
RELB	3.007213	5.745798	101.00085	0.0000046	0.0012883
TAF4B	3.014949	3.286624	92.77776	0.0000063	0.0014380
SH2B3	3.016999	5.564816	47.23800	0.0000959	0.0044695
PCDH8	3.023577	2.109310	32.17253	0.0007661	0.0142109
TFPI2	3.045211	7.289627	76.41806	0.0000156	0.0019665
SAMHD1	3.052257	6.155858	33.54926	0.0003252	0.0090658
GFPT2	3.053507	7.114968	55.27068	0.0000536	0.0032875
IL12A	3.074159	1.954999	35.21462	0.0018710	0.0237584
NFKB2	3.074821	5.527933	111.23830	0.0000030	0.0012769
MYO10	3.075920	5.670992	51.52942	0.0000696	0.0037609
SLC25A25	3.094355	5.643307	49.35799	0.0000816	0.0040633
PAPPA	3.106189	7.907271	78.09810	0.0000144	0.0019055
KCNJ6	3.107220	3.589969	66.83040	0.0000262	0.0025480
PLA2G4A	3.110495	4.074551	82.71147	0.0000115	0.0016253
IDI2-AS1	3.112656	1.917110	26.86395	0.0021878	0.0261013
CDC42EP2	3.119416	4.920009	43.94273	0.0001248	0.0052069
NBPF10	3.123370	5.585064	58.08067	0.0000445	0.0030414
PARP10	3.156709	4.824737	34.79916	0.0002864	0.0084898
NFKBIZ	3.159083	7.121925	67.68861	0.0000249	0.0025076
CD83	3.173820	4.440632	100.41670	0.0000049	0.0013075
PER2	3.177066	3.949798	105.20435	0.0000038	0.0012869
SUSD3	3.177775	1.913574	49.11554	0.0019182	0.0240671
NPIPB9	3.187425	3.056459	85.96106	0.0000090	0.0015377
TNFSF4	3.194547	4.449263	39.82799	0.0001777	0.0065217
CSRNP1	3.209089	6.393243	77.56168	0.0000148	0.0019306
LIF	3.218333	3.313136	68.51894	0.0000238	0.0024308
CDCP1	3.221546	3.220219	40.95561	0.0001608	0.0061107
CFAP43	3.236729	2.165087	49.14447	0.0002905	0.0085601
IFI6	3.245873	9.114637	16.84248	0.0030030	0.0316902
CYP1B1	3.250809	7.104491	78.42151	0.0000141	0.0018880
HELZ2	3.260663	3.448995	29.49406	0.0005059	0.0113044
IFIH1	3.261873	4.786974	19.15159	0.0020406	0.0249842
MAP3K8	3.271886	4.537469	125.90809	0.0000018	0.0010564
DDX58	3.283058	6.746199	25.90700	0.0007804	0.0143064
MYCT1	3.289963	2.046555	40.95518	0.0006164	0.0125473
CDH16	3.290525	1.742021	60.36658	0.0044961	0.0403046
SIX4	3.320190	3.895493	92.89530	0.0000071	0.0015101
NR1D1	3.343418	4.357002	106.64788	0.0000039	0.0012869
IFITM1	3.349915	8.961878	31.36005	0.0004105	0.0101815
MAFF	3.370586	5.316654	148.11264	0.0000009	0.0008348
TRIM14	3.388914	4.091813	23.23787	0.0011119	0.0174687
PTPRN	3.400174	5.267114	87.46905	0.0000092	0.0015377
PLAUR	3.405416	6.861024	104.07963	0.0000047	0.0012892
ANKS4B	3.408031	2.135298	51.93580	0.0002362	0.0075737
NFKBIA	3.417202	8.391397	107.47928	0.0000038	0.0012869
BST2	3.420476	7.307547	28.62527	0.0005597	0.0118432
CDK5R1	3.428745	4.033448	61.98541	0.0000348	0.0028119
MLKL	3.442330	2.640487	32.79267	0.0003520	0.0094101
GIPC3	3.444105	2.761143	35.57037	0.0002652	0.0081698
NPC1L1	3.472580	1.880101	42.48278	0.0013512	0.0196696
MYRFL	3.473980	3.090140	112.05350	0.0000029	0.0012769
CXCR1	3.476321	1.651404	65.32856	0.0057019	0.0469329
PCDH15	3.477425	2.628085	60.98567	0.0000370	0.0028841
SNAI1	3.501171	3.290060	116.77807	0.0000025	0.0012520
ANKRD33B	3.521136	3.588617	84.47745	0.0000106	0.0015867
USP18	3.526600	5.093084	22.54242	0.0012256	0.0185422
PTX3	3.554543	8.390962	123.98638	0.0000020	0.0010944
NFATC2	3.555795	3.933467	108.29201	0.0000037	0.0012869
SERPINE1	3.556188	10.606702	103.55315	0.0000043	0.0012883
SLC2A5	3.566019	3.689098	139.12562	0.0000012	0.0008663
MICB	3.587570	4.564095	128.86532	0.0000017	0.0010207
ZBTB2	3.600436	6.397979	128.33353	0.0000018	0.0010564
LINC01823	3.619946	1.710207	70.23833	0.0032122	0.0329840
SLC12A8	3.620080	6.029256	138.55951	0.0000012	0.0008663
SAMD9	3.629801	5.398846	25.32834	0.0008405	0.0149144
IRF8	3.652257	3.459020	129.81346	0.0000016	0.0010207
STC1	3.653529	4.152861	114.32324	0.0000030	0.0012769
APCDD1L	3.695406	2.896546	63.34529	0.0000321	0.0027505
IFI27	3.706511	5.887802	13.31120	0.0058680	0.0476806
GAL3ST1	3.711185	2.265829	88.74739	0.0000349	0.0028119
SRGN	3.730504	3.888739	90.97631	0.0000079	0.0015101
BIRC3	3.746385	3.629215	142.35202	0.0000011	0.0008348
NR4A3	3.746540	4.579866	99.92274	0.0000055	0.0014052
SAA1	3.753236	2.059358	53.31650	0.0001962	0.0069235
NXPE2	3.755393	2.052772	74.76876	0.0002086	0.0071561
CXCL8	3.764355	3.864053	93.14546	0.0000072	0.0015101
ACTBL2	3.808624	3.464013	75.19980	0.0000166	0.0019783
FOSB	3.811074	3.547716	90.06315	0.0000082	0.0015101
TNC	3.811429	8.709608	29.60629	0.0004994	0.0112467
SPOCD1	3.815799	3.920872	142.58956	0.0000011	0.0008348
CXCL3	3.824323	3.424551	90.05022	0.0000083	0.0015101
HAS1	3.840127	2.411141	95.33842	0.0000057	0.0014052
NR4A1AS	3.850720	2.651442	58.71612	0.0000427	0.0030190
ZC3H12A	3.904393	5.451827	178.02256	0.0000004	0.0007127
SENP3-EIF4A1	3.910008	2.840661	45.47944	0.0001101	0.0048017
SUCNR1	3.918909	6.828456	151.63876	0.0000009	0.0008217
HLF	3.969301	2.010502	61.39614	0.0001951	0.0069235
BAAT	3.986116	1.875604	82.83832	0.0005595	0.0118432
ISG15	3.987277	8.765821	28.31308	0.0005807	0.0120834
HSPA6	4.021950	5.075571	57.94640	0.0000449	0.0030492
ISG20	4.034635	3.041143	30.04930	0.0004749	0.0110002
IFIT2	4.073136	5.933346	24.85427	0.0008941	0.0154317
IFI44	4.086988	4.919038	28.00651	0.0006023	0.0123602
NR4A1	4.159769	6.218755	192.68473	0.0000003	0.0007000
CD68	4.171354	3.317853	34.80694	0.0002861	0.0084898
DHX58	4.190837	2.712811	16.60052	0.0031338	0.0324848
HIVEP2	4.198906	6.659401	48.31647	0.0000882	0.0042472
NT5E	4.316077	7.310700	108.33623	0.0000040	0.0012869
C7orf61	4.365896	2.734189	77.09207	0.0000151	0.0019319
NR4A2	4.367729	3.981776	191.45573	0.0000003	0.0007000
FERMT3	4.484359	2.883749	103.27124	0.0000046	0.0012883
IRF7	4.489884	5.679134	62.13961	0.0000345	0.0028119
TGIF2-RAB5IF	4.494917	4.362682	190.74201	0.0000003	0.0007000
GDF15	4.512745	6.839520	173.03468	0.0000005	0.0007127
CD200R1	4.523281	2.018138	70.30699	0.0000674	0.0037157
GREM1	4.546835	6.032808	90.62883	0.0000080	0.0015101
NUAK2	4.662422	5.571280	189.51363	0.0000003	0.0007000
PTAFR	4.698314	2.295618	58.87163	0.0000423	0.0030190
HAS2	4.774514	5.249723	98.86211	0.0000057	0.0014052
GALNT15	4.843532	3.923216	119.59236	0.0000027	0.0012769
SPDYA	4.964848	3.560782	187.05871	0.0000004	0.0007000
CXCL1	4.990861	2.433813	130.67746	0.0000016	0.0010207
OSM	5.000936	2.248774	46.25914	0.0001035	0.0046794
TNFAIP3	5.158030	8.324103	97.05961	0.0000061	0.0014197
MRC1	5.160553	3.048629	175.47488	0.0000005	0.0007127
MX2	5.179423	4.265989	16.50202	0.0031890	0.0328799
CCL7	5.291829	4.389444	162.54788	0.0000007	0.0007268
IL1B	5.353070	2.593641	121.05582	0.0000021	0.0011397
IFIT3	5.363579	6.476869	32.11417	0.0003783	0.0097807
RSAD2	5.381729	4.795030	15.69902	0.0036876	0.0358349
CXCL2	5.393316	4.112167	241.10541	0.0000001	0.0007000
CA9	5.446761	3.354625	105.39236	0.0000044	0.0012883
IFNB1	5.579821	2.416278	14.13598	0.0049686	0.0431032
CMPK2	5.739321	4.968540	18.36468	0.0023186	0.0270494
IFI44L	5.886140	5.480482	29.97991	0.0004786	0.0110238
OAS3	6.040390	5.476378	55.45416	0.0000530	0.0032675
ANGPTL4	6.667607	7.693979	263.86127	0.0000001	0.0007000
MX1	6.839104	8.213029	71.14538	0.0000206	0.0022828
OAS1	6.914038	6.380700	55.83812	0.0000516	0.0032300
OAS2	7.149848	5.743360	38.37334	0.0002029	0.0070229
PTGS2	7.172085	7.222030	227.27911	0.0000002	0.0007000
IL11	7.811430	5.185583	285.28029	0.0000001	0.0007000

Non-thresholded Gene Set Enrichment Analysis

Conduct non-thresholded gene set enrichment analysis using the ranked set of genes from Assignment #2.

1.What method did you use? What genesets did you use? Make sure to specify versions and cite your methods.

I used GSEA4.2.3 in this part; Cytoscape 3.9.1, its Enrichment Map application and AutoAnnotation (1.3.5) application for the downstream analysis.

2.Summarize your enrichment results.

knitr::kable(ranked_gene_list_na_pos_versus_na_neg_1648855165869, caption = 'Table 2. Ranked Gene List Virus vs. Mock')

Table 2. Ranked Gene List Virus vs. Mock

NAME	SCORE
IL11	7.811430
PTGS2	7.172085
OAS2	7.149848
OAS1	6.914038
MX1	6.839104
ANGPTL4	6.667607
OAS3	6.040390
IFI44L	5.886140
CMPK2	5.739321
IFNB1	5.579821
CA9	5.446761
CXCL2	5.393316
RSAD2	5.381730
IFIT3	5.363579
IL1B	5.353070
CCL7	5.291829
MX2	5.179423
MRC1	5.160553
TNFAIP3	5.158030
OSM	5.000936
CXCL1	4.990861
SPDYA	4.964848
GALNT15	4.843532
HAS2	4.774514
PTAFR	4.698314
NUAK2	4.662423
GREM1	4.546835
CD200R1	4.523281
GDF15	4.512745
TGIF2-RAB5IF	4.494917
IRF7	4.489884
FERMT3	4.484359
NR4A2	4.367728
C7orf61	4.365896
NT5E	4.316078
HIVEP2	4.198906
DHX58	4.190837
CD68	4.171354
NR4A1	4.159769
IFI44	4.086988
IFIT2	4.073136
ISG20	4.034635
HSPA6	4.021950
ISG15	3.987277
BAAT	3.986116
HLF	3.969301
SUCNR1	3.918909
SENP3-EIF4A1	3.910008
ZC3H12A	3.904393
NR4A1AS	3.850720
HAS1	3.840127
CXCL3	3.824323
SPOCD1	3.815799
TNC	3.811428
FOSB	3.811074
ACTBL2	3.808624
CXCL8	3.764355
NXPE2	3.755393
SAA1	3.753236
NR4A3	3.746540
BIRC3	3.746385
SRGN	3.730504
GAL3ST1	3.711185
IFI27	3.706511
APCDD1L	3.695406
STC1	3.653529
IRF8	3.652257
SAMD9	3.629801
SLC12A8	3.620080
LINC01823	3.619946
ZBTB2	3.600436
MICB	3.587570
SLC2A5	3.566019
SERPINE1	3.556188
NFATC2	3.555795
PTX3	3.554543
USP18	3.526600
ANKRD33B	3.521136
SNAI1	3.501171
PCDH15	3.477425
CXCR1	3.476321
MYRFL	3.473980
NPC1L1	3.472580
GIPC3	3.444105
MLKL	3.442330
CDK5R1	3.428745
BST2	3.420476
NFKBIA	3.417202
ANKS4B	3.408031
PLAUR	3.405416
PTPRN	3.400174
TRIM14	3.388913
MAFF	3.370586
IFITM1	3.349915
NR1D1	3.343418
SIX4	3.320190
CDH16	3.290525
MYCT1	3.289963
DDX58	3.283058
MAP3K8	3.271886
IFIH1	3.261873
HELZ2	3.260663
CYP1B1	3.250809
IFI6	3.245873
CFAP43	3.236729
CDCP1	3.221546
LIF	3.218332
CSRNP1	3.209090
TNFSF4	3.194547
NPIPB9	3.187425
SUSD3	3.177775
PER2	3.177066
CD83	3.173820
NFKBIZ	3.159083
PARP10	3.156709
NBPF10	3.123370
CDC42EP2	3.119416
IDI2-AS1	3.112656
PLA2G4A	3.110495
KCNJ6	3.107220
PAPPA	3.106189
SLC25A25	3.094355
MYO10	3.075920
NFKB2	3.074822
IL12A	3.074159
GFPT2	3.053507
SAMHD1	3.052257
TFPI2	3.045211
PCDH8	3.023577
SH2B3	3.016999
TAF4B	3.014949
RELB	3.007213
FNDC11	3.003023
EGR2	2.997124
PFKFB4	2.996145
ADM5	2.995367
APLN	2.991301
TMEM255B	2.982863
IL6	2.982850
NPIPB6	2.977480
TLR4	2.977475
TNFRSF6B	2.973553
LINC01119	2.971468
OSMR	2.968027
SLC20A1	2.959516
ZSWIM4	2.947280
AGTR1	2.936738
ADCY10	2.934266
GCH1	2.930393
FOS	2.924209
TMEM119	2.916719
IPMK	2.909372
TMEM158	2.907376
IFIT1	2.897333
FAM83G	2.890823
PPP1R15A	2.888216
PTGS1	2.871569
ATP10A	2.857127
SAMD9L	2.854908
H2BC6	2.848198
ANXA10	2.847749
ICAM1	2.844774
LOX	2.837510
ATF3	2.834750
HAP1	2.828557
GPR87	2.819893
SLC5A3	2.807390
CDC14A	2.798065
ARRDC3	2.797668
APOL3	2.797154
KCNG1	2.794918
TMEM200A	2.789991
FOSL1	2.786567
PER1	2.773211
SPHK1	2.772888
RFLNA	2.764764
GALNT12	2.762916
ARHGEF28	2.759261
CCNL1	2.752683
RBM47	2.744715
JUNB	2.744661
IP6K3	2.727148
PTGES	2.722689
BHLHE41	2.722265
PRR5L	2.722209
PLOD2	2.720926
SLC19A2	2.718296
H2BC18	2.711889
CPA4	2.708803
ZBTB21	2.703003
INHBE	2.700693
ADGRE5	2.699674
CHD2	2.697284
CCL2	2.692769
BMP6	2.691649
TM4SF1	2.691544
WNK4	2.682955
GABRR2	2.682761
SERPINB2	2.677729
SP100	2.676217
SELPLG	2.668810
KCNN1	2.667134
ITGA5	2.665103
PDCD1LG2	2.657190
SBNO2	2.656249
SGK1	2.647606
H2BC8	2.643823
PARP14	2.642709
TMED7-TICAM2	2.639298
PMAIP1	2.637589
HOXA5	2.628181
TNFRSF10D	2.620613
BMPR1B	2.619521
GRB7	2.610120
TNFSF9	2.605547
IL1R1	2.605356
HERC6	2.604753
CD101	2.589927
F2RL1	2.589487
ADIRF-AS1	2.579662
CSF1	2.579402
STC2	2.574370
APOL6	2.571367
SPINT1	2.569089
OVGP1	2.567849
PHLDA2	2.549979
CPM	2.545456
VEGFC	2.535167
UGCG	2.518274
KLF10	2.515128
TRAF1	2.514945
LOXL3	2.511423
FNIP2	2.511309
SLC2A3	2.509515
TIGD3	2.508575
MEDAG	2.503234
EDEM1	2.498534
BHLHE40	2.496503
KLF5	2.485018
IL15RA	2.483720
PTGER4	2.483473
KLF4	2.478537
PDE10A	2.477695
CA12	2.469995
SLCO2A1	2.466396
DUSP4	2.462814
SOX17	2.458071
NEFM	2.456494
MAPK13	2.450262
HIVEP1	2.437602
LOXL2	2.435605
NBPF19	2.433163
INSYN2B	2.430209
BCL6	2.422277
PARP9	2.414755
MYO3A	2.414730
NR6A1	2.414602
TET3	2.410728
CXCL6	2.410656
TNFRSF1B	2.408509
TG	2.407485
TPBG	2.407003
HLA-E	2.405630
CREBRF	2.394751
CIART	2.392362
RGS4	2.388592
FRMD6	2.387872
MALL	2.383326
INHBA	2.383219
IRF1	2.379943
APOL1	2.379876
ADAM32	2.376574
AMIGO2	2.368723
LSMEM1	2.361432
MCTP2	2.360615
JUN	2.358727
ULBP2	2.358103
BCAR3	2.356021
BCL3	2.352478
ELF3	2.340596
CD44	2.340378
INTS6	2.335218
TRIM38	2.333957
IRAK2	2.332145
SLC22A3	2.328724
SLC43A3	2.324096
EPHA2	2.323694
PDK4	2.321624
TAP1	2.318335
SLC2A9	2.313958
SULF1	2.309025
HTR7	2.306583
ALDH1A3	2.304578
CFB	2.294208
TRIM25	2.294127
DUSP1	2.292234
SERPINB8	2.291079
BRPF1	2.289519
GPR176	2.287500
DDIT3	2.282792
ITGA4	2.280581
RBM15	2.273480
HES1	2.272304
STEAP1	2.269506
SPRED1	2.268266
SLC7A5	2.268056
ARSI	2.258777
RASGRF2	2.257768
DRAM1	2.255817
ETV4	2.255293
DUSP6	2.247526
TNFAIP2	2.246920
DTX3L	2.238600
SMOX	2.238389
FOXN2	2.235189
SPRED3	2.232555
MFAP3L	2.230693
CLK4	2.230614
SNAPC1	2.224079
GPBP1	2.221672
WAKMAR2	2.221539
CACTIN	2.216597
SMURF1	2.206765
ATP8B1	2.201638
IL1RL1	2.200511
TBC1D2	2.199856
NEDD9	2.198391
ACHE	2.184266
PTGIS	2.183773
LRRC8E	2.181391
SEL1L3	2.178554
KCNAB1	2.174609
HFE	2.173138
SEC24A	2.171192
NFKBID	2.170539
GADD45B	2.169566
CHD1	2.167425
ZBTB10	2.166943
HS6ST2	2.158807
EIF2AK2	2.155542
LDB2	2.155333
STARD13	2.146103
GBP3	2.142594
TYMP	2.142315
THY1	2.139841
NBPF26	2.135125
RXFP1	2.133374
TENT5C	2.132303
IL33	2.129479
THSD1	2.128001
ARHGAP20	2.123484
SLC38A5	2.122949
NRG3	2.120995
KLF11	2.114600
ERRFI1	2.113944
MVP	2.111094
C1QTNF1	2.109298
DPP4	2.104114
TMEM87B	2.099924
PDE7A	2.096324
IFRD1	2.095692
ZNF317	2.095386
UBASH3B	2.093595
NBPF14	2.093447
HOXA-AS2	2.088457
CDH6	2.086026
SH3RF1	2.084813
FGF7	2.083364
SQSTM1	2.082316
KLF9	2.079559
ADCY7	2.076348
RGS16	2.075771
CLCF1	2.075358
NPIPB15	2.073422
RAPGEF2	2.072268
PCSK9	2.069441
SKIL	2.067251
DOK5	2.067119
ITGA2	2.062052
ZNF844	2.061578
PDZD2	2.058617
TRIM22	2.055730
PFKFB3	2.054620
BAIAP2L1	2.054319
ADM2	2.052314
DBP	2.048629
PIK3CD	2.048266
HAPLN3	2.047483
EMP1	2.044095
LIPG	2.043150
H2BC5	2.042077
EVC2	2.040074
HRH1	2.039099
EGR1	2.037634
TLE1	2.036129
KCNE4	2.032976
CASP4	2.031420
ARRDC2	2.028687
PIGA	2.025300
RSRC2	2.024864
PIM3	2.022238
GTF2IRD1	2.022119
LRIG3	2.022030
MYD88	2.019954
ERO1A	2.009337
RLF	2.009219
TGFBI	2.008175
PTBP3	2.004432
ACOT13	-2.000114
PLK1	-2.000453
CPVL	-2.005104
FANCL	-2.006840
CHURC1-FNTB	-2.009534
UQCR10	-2.010785
HADH	-2.010848
SVIP	-2.011910
PPP1R3C	-2.018053
IL17B	-2.019427
CHCHD5	-2.019536
ATP5MPL	-2.020557
TIMM8B	-2.021806
MYL3	-2.022303
ATP5MC1	-2.023177
GSTM4	-2.024015
DHRS11	-2.024969
GJA5	-2.025338
SKA3	-2.028284
ETFRF1	-2.029499
PIFO	-2.030697
DNAJC15	-2.036522
RDH5	-2.037272
SMDT1	-2.037491
PET100	-2.043188
HACD1	-2.043966
ERH	-2.046144
NIFK-AS1	-2.046841
PPP1R14C	-2.047443
ATP5MF	-2.049363
NEXN	-2.052929
INKA2-AS1	-2.054012
NSMCE4A	-2.054613
ST7-AS1	-2.056492
MMP15	-2.056655
ABHD11	-2.056984
PLCXD3	-2.058581
FAM20A	-2.059499
MYLK	-2.060309
COX8A	-2.061003
ACYP1	-2.061078
NDUFC1	-2.062849
DGCR6	-2.064497
SH3RF2	-2.067586
TMEM144	-2.068687
PARP1	-2.069997
ATP5PD	-2.070352
ICA1	-2.073635
HIGD2A	-2.075338
CDCA7	-2.075812
FAM229B	-2.080910
PLPP7	-2.082147
PHACTR1	-2.086106
DOK7	-2.086878
GNG7	-2.087833
EMP2	-2.088005
ASB2	-2.088868
GTSE1	-2.089318
EFCAB7	-2.091420
KLHL3	-2.095120
CDKN2C	-2.096007
MYBPC3	-2.098119
GUCY1A1	-2.098464
ATP5MC3	-2.098677
IL20RA	-2.099056
NAP1L3	-2.099201
MRPL53	-2.101326
ANAPC16	-2.104280
MGST3	-2.109753
BEX2	-2.111248
ITM2A	-2.118308
CMC4	-2.118674
NDUFB2	-2.118844
UQCRQ	-2.122164
SYNM	-2.122636
ATP5ME	-2.123243
SHCBP1	-2.129380
HMGN5	-2.130325
GLIDR	-2.130896
DECR1	-2.132020
PRC1	-2.133292
SLC5A1	-2.133719
TMEM97	-2.134051
DES	-2.134094
DLGAP1-AS1	-2.134387
ULK4	-2.138354
LINC02762	-2.143704
LINC01351	-2.148929
MTURN	-2.152774
PMEL	-2.153426
MDP1	-2.154549
ADCY5	-2.158902
NDUFS6	-2.162245
USH1C	-2.162887
INKA2	-2.162963
DNAJC28	-2.164137
TAFA2	-2.164442
MPC1	-2.165892
PCBD1	-2.167003
HAND2-AS1	-2.167011
PLN	-2.167092
ROGDI	-2.167942
MYL9	-2.170793
HMGN2	-2.174406
C10orf71	-2.176344
LINC00880	-2.177140
HMGCLL1	-2.178475
RBMS3-AS3	-2.180075
DAND5	-2.181967
SSPN	-2.183134
REXO5	-2.195596
COX6C	-2.195835
LINC00526	-2.197931
SELENOW	-2.198793
ACADSB	-2.198825
CDC20	-2.200800
VSNL1	-2.201836
ACAT1	-2.204879
GON7	-2.209077
KCNQ2	-2.214763
CDC6	-2.216078
SYNJ2BP-COX16	-2.221443
PLK4	-2.221475
SLC2A8	-2.222631
SCHIP1	-2.222649
TBX20	-2.225745
LYPD6	-2.228899
YPEL1	-2.232118
KIF22	-2.232446
ANKRD1	-2.238789
CTF1	-2.240603
UNC45B	-2.241744
BCL2A1	-2.242443
SRP14-AS1	-2.245190
LYRM9	-2.250067
NIPSNAP3B	-2.253375
BANCR	-2.253846
DERL3	-2.255450
HAND2	-2.255680
ACOT1	-2.259996
TECRL	-2.264283
CAMK2A	-2.271184
CRIP2	-2.272728
COX7B	-2.281664
KIAA0319	-2.281730
HAND1	-2.281999
S100A6	-2.287949
CORO6	-2.289831
BIK	-2.292042
CCND2-AS1	-2.295584
BOLA1	-2.296717
NDUFA3	-2.302154
ACSM5	-2.303018
DRD1	-2.305130
COL21A1	-2.309664
ATP5PF	-2.312218
GP1BB	-2.314509
MORN2	-2.319151
TK1	-2.320188
CDCA5	-2.322462
LRRC52-AS1	-2.324422
LINC01778	-2.327603
FPGT	-2.329109
TMOD1	-2.329743
CLIC5	-2.332800
PDE6B	-2.333192
C17orf97	-2.335326
FOXM1	-2.340321
TRDN-AS1	-2.340616
CRYAB	-2.344243
HSD17B8	-2.345639
DNAAF3	-2.348180
UBE2C	-2.349332
TAGLN3	-2.354777
ZSCAN16-AS1	-2.356235
MRPS28	-2.358498
FN3K	-2.364778
RPA3	-2.365246
NTF4	-2.377098
VIPR1	-2.382483
EPHX2	-2.384289
HSPB1	-2.385072
C14orf180	-2.386624
RCSD1	-2.389719
C11orf74	-2.390511
SLC30A3	-2.395008
PHYHD1	-2.395036
CENPH	-2.395726
SLC8A1	-2.406968
TRAPPC6A	-2.409063
NES	-2.412128
NEBL	-2.413640
TMEM141	-2.417552
LRRC10	-2.418899
NUSAP1	-2.423946
GSG1	-2.424480
KCNS2	-2.425896
PHOSPHO2	-2.427787
EXOC3-AS1	-2.430176
LINC02384	-2.433270
IDNK	-2.433926
LRRCC1	-2.437214
SFRP2	-2.438680
CLYBL	-2.443257
DUSP27	-2.443680
TSTD1	-2.443933
HJURP	-2.451450
MTERF2	-2.454024
ACOT2	-2.463990
PRADC1	-2.464355
PHACTR3	-2.466546
RPE65	-2.467311
ADHFE1	-2.470553
ZNF793-AS1	-2.482754
APOBEC2	-2.495307
CCNB2	-2.500282
GIHCG	-2.502606
SMIM5	-2.507403
UPK1B	-2.518697
C11orf1	-2.523570
CDK1	-2.528634
MINCR	-2.531948
PNMT	-2.532905
CKAP2L	-2.533517
DEPDC1	-2.538446
COX7C	-2.538748
FERMT1	-2.540029
RMI2	-2.542336
TYMSOS	-2.551361
NEK2	-2.561090
SLC26A9	-2.565358
CRABP2	-2.565913
MIR1-1HG-AS1	-2.567849
PKIA	-2.570428
ALDOC	-2.573856
PKMYT1	-2.575518
GPR183	-2.580100
SFRP5	-2.580538
RRM2	-2.581340
BRINP2	-2.587693
TMEM163	-2.592041
BIRC5	-2.603424
CASQ1	-2.614019
NDUFB1	-2.617046
C11orf71	-2.622072
TMEM71	-2.625232
MLIP	-2.626909
TYRP1	-2.631008
UBE2E1	-2.633303
PDE1A	-2.636327
SLC27A6	-2.640879
DTL	-2.641167
SGCA	-2.644098
GPX3	-2.652738
MYZAP	-2.654654
PLAC1	-2.658369
CASQ2	-2.660241
CAVIN3	-2.661827
ANLN	-2.662587
SPHKAP	-2.668391
IGSF5	-2.672417
SYNPO2L	-2.672782
GPR22	-2.683250
SMYD1	-2.687409
SORCS3	-2.687721
LINC00881	-2.692807
HRH2	-2.694184
PEBP4	-2.695043
CDCA8	-2.698342
CEP55	-2.708550
SPX	-2.708569
AMT	-2.719618
DIRAS3	-2.722534
CDC45	-2.726066
POLE2	-2.734335
TRDN	-2.737878
NMRK2	-2.747681
PIMREG	-2.749342
EPN3	-2.749571
FPGT-TNNI3K	-2.753526
REC114	-2.761811
SH3BGR	-2.764689
MOG	-2.766072
CSPG5	-2.786076
H4C3	-2.794520
SMIM1	-2.796013
SRPK3	-2.800608
SLC15A2	-2.804699
SLC38A3	-2.806756
ASF1B	-2.817701
TNNT2	-2.820532
RAB9B	-2.823723
EMC10	-2.824767
IMMP1L	-2.829254
HMGB2	-2.830279
FMC1	-2.830632
LINC01456	-2.832458
NCAPH	-2.854564
ENPP5	-2.856968
KIF2C	-2.860460
CRIP1	-2.865284
VSTM2L	-2.866543
LGALS3	-2.871758
LEFTY2	-2.880727
CSRP3	-2.882775
C11orf52	-2.904686
MCM5	-2.908502
NREP	-2.911058
RXRG	-2.913305
UBE2T	-2.922022
HRC	-2.948080
NEIL3	-2.948272
SGO1	-2.953492
PTGES3L	-2.953571
AQP10	-2.967106
LINC01405	-2.969873
G0S2	-2.979050
FRMD3	-2.990653
TOP2A	-3.004569
HOPX	-3.009609
C1orf105	-3.013779
NUDT7	-3.015060
PANCR	-3.015240
COL9A1	-3.024658
SPC24	-3.025167
ZWINT	-3.030731
BBOX1-AS1	-3.034916
DHFR	-3.035134
CRYM	-3.048275
SELENOP	-3.060758
KIF20A	-3.066232
CAV3	-3.066379
GABRA4	-3.068427
CDCA3	-3.086259
NPPA	-3.091703
SLC5A12	-3.096242
FGF13-AS1	-3.097264
PPP1R1C	-3.100553
ITGB1BP2	-3.103756
AIF1L	-3.108962
PLCB2	-3.129927
CALN1	-3.145096
TESC	-3.150083
NUF2	-3.151356
SPSB4	-3.155675
LSMEM2	-3.164595
PPP1R1A	-3.171572
KLHDC9	-3.218902
DMAC1	-3.234254
FAM133A	-3.237091
CHCHD10	-3.261912
NDC80	-3.269491
FSD2	-3.274605
OIP5	-3.282617
FITM1	-3.291142
TRIM54	-3.298866
CENPU	-3.303800
CDKN3	-3.334427
AURKB	-3.351708
ATP6V1G2	-3.357918
DLGAP5	-3.375682
GPD1	-3.377976
SMPX	-3.395799
LMOD2	-3.403714
HSPB3	-3.409678
MYH7	-3.415903
C1QL1	-3.445765
TNNI3	-3.479622
FABP3	-3.492141
MARCHF11	-3.530975
MB	-3.542870
CD36	-3.544471
SLC35D3	-3.553160
LINC01182	-3.561014
LDHD	-3.576655
LINC01611	-3.581984
MIR133A1HG	-3.586468
ACTC1	-3.599775
MYLK-AS1	-3.614126
PCLAF	-3.618731
GINS2	-3.632645
LDB3	-3.633489
GJD2	-3.648797
TNNI1	-3.649594
NAV2-AS2	-3.659571
SUSD2	-3.664531
RAD51AP1	-3.668636
CORIN	-3.695186
CPNE5	-3.696150
HSPB7	-3.772049
NME5	-3.772923
MYL4	-3.789321
ACE2	-3.792261
FGF12	-3.795245
TROAP	-3.795809
CCDC34	-3.807975
CKMT2	-3.843017
ODAM	-3.875695
MYL7	-3.935387
ADPRHL1	-3.938632
S100A8	-3.987699
MAOB	-4.013483
TNMD	-4.017589
TMSB15A	-4.023837
MSS51	-4.049343
CENPM	-4.064744
TCAP	-4.067439
PBK	-4.114213
COX6A2	-4.168300
IRX4-AS1	-4.282455
TNNC1	-4.285373
LINC02502	-4.298163
FAM111B	-4.336571
SPC25	-4.366327
FXYD1	-4.430059
ACTA1	-4.549569
HHATL	-4.724839
METTL7B	-4.984910
ALAS2	-5.044219
FBXL22	-5.289780
MYL2	-5.499683
KCNIP2	-5.719563
PGAM2	-5.823109

• 16035 gene sets with size larger than 200 or smaller than 15 were filtered out from a total of 16746, the remaining 711 gene sets were used in this analysis. We used a stricter boundary to obtain more rigorous results. We selected the permutation number of 1000, which has a suitable running time for the program.

• The Positive Phenotype (na_pos):

Table 3. Enrichment Plot of the Top 20 Gene Sets Ranked in the Positive(Virus) Phenotype

517 out of 711 gene sets are returned in the Virus (na_pos) sub-type. 421 gene sets are significant at FDR < 25%. 304 gene sets are significantly enriched at nominal p-value < 1%. 366 gene sets are significantly enriched at nominal p-value < 5%. The most related gene set in this sub-type according to the analysis is DEFENSE RESPONSE GOBP GO:0006952, with an enrichment score (ES) of 0.5994537 and a normalized enrichment score (NES) of 4.323445.

Figure 1. Profile of the Running ES Score & Positions of DEFENSE RESPONSE GOBP GO:0006952 on the Rank Ordered List

Figure 2. Random ES Distribution of DEFENSE RESPONSE GOBP GO:0006952

knitr::kable(DEFENSE_RESPONSE_GOBP, caption = 'Table 4. DEFENSE RESPONSE GOBP')

Table 4. DEFENSE RESPONSE GOBP

NAME	RANK.IN.GENE.LIST	RANK.METRIC.SCORE	RUNNING.ES	CORE.ENRICHMENT
OAS2	2	7.149848	0.0245612	Yes
OAS1	3	6.914038	0.0508740	Yes
MX1	4	6.839104	0.0769017	Yes
OAS3	6	6.040390	0.0985651	Yes
IFI44L	7	5.886140	0.1209661	Yes
IFNB1	9	5.579821	0.1408767	Yes
CXCL2	11	5.393316	0.1600776	Yes
RSAD2	12	5.381730	0.1805589	Yes
IFIT3	13	5.363579	0.2009711	Yes
IL1B	14	5.353070	0.2213434	Yes
CCL7	15	5.291829	0.2414825	Yes
MX2	16	5.179423	0.2611939	Yes
CXCL1	20	4.990861	0.2762141	Yes
PTAFR	24	4.698314	0.2901210	Yes
IRF7	30	4.489884	0.3005857	Yes
IFIT2	40	4.073136	0.3041663	Yes
ISG20	41	4.034635	0.3195210	Yes
ISG15	43	3.987277	0.3333709	Yes
CXCL3	51	3.824323	0.3386536	Yes
CXCL8	56	3.764355	0.3476816	Yes
SAA1	58	3.753236	0.3606409	Yes
IRF8	66	3.652257	0.3652688	Yes
MICB	71	3.587570	0.3736240	Yes
SERPINE1	73	3.556188	0.3858333	Yes
PTX3	75	3.554543	0.3980364	Yes
CXCR1	80	3.476321	0.4059682	Yes
BST2	86	3.420476	0.4123630	Yes
TRIM14	91	3.388913	0.4199622	Yes
IFITM1	93	3.349915	0.4313865	Yes
DDX58	98	3.283058	0.4385829	Yes
IFIH1	100	3.261873	0.4496721	Yes
IFI6	103	3.245873	0.4593759	Yes
TNFSF4	108	3.194547	0.4662354	Yes
CD83	112	3.173820	0.4743406	Yes
NFKB2	123	3.074822	0.4727974	Yes
IL12A	124	3.074159	0.4844968	Yes
SAMHD1	126	3.052257	0.4947883	Yes
RELB	131	3.007213	0.5009348	Yes
IL6	138	2.982850	0.5043396	Yes
TLR4	140	2.977475	0.5143465	Yes
TNFRSF6B	141	2.973553	0.5256630	Yes
GCH1	148	2.930393	0.5288683	Yes
FOS	149	2.924209	0.5399969	Yes
IFIT1	153	2.897333	0.5470498	Yes
ICAM1	161	2.844774	0.5486047	Yes
APOL3	169	2.797154	0.5499783	Yes
FOSL1	172	2.786567	0.5579342	Yes
ADGRE5	191	2.699674	0.5443672	Yes
CCL2	193	2.692769	0.5532907	Yes
SP100	199	2.676217	0.5568531	Yes
PMAIP1	209	2.637589	0.5549704	Yes
TNFRSF10D	211	2.620613	0.5636192	Yes
F2RL1	218	2.589487	0.5655270	Yes
LOXL3	231	2.511423	0.5591907	Yes
CXCL6	258	2.410656	0.5339279	Yes
TNFRSF1B	259	2.408509	0.5430939	Yes
HLA-E	262	2.405630	0.5496001	Yes
INHBA	268	2.383219	0.5520474	Yes
IRF1	269	2.379943	0.5611048	Yes
APOL1	270	2.379876	0.5701619	Yes
ULBP2	276	2.358103	0.5725136	Yes
ELF3	279	2.340596	0.5787722	Yes
CD44	280	2.340378	0.5876790	Yes
TRIM38	282	2.333957	0.5952369	Yes
CFB	293	2.294208	0.5907229	Yes
TRIM25	294	2.294127	0.5994537	Yes
TRIM22	381	2.055730	0.4933699	No
PIK3CD	386	2.048266	0.4958670	No
HRH1	392	2.039099	0.4970047	No
EGR1	393	2.037634	0.5047594	No
MYD88	403	2.019954	0.5005262	No
CAMK2A	549	-2.271184	0.3171166	No
EPHX2	588	-2.384289	0.2758595	No
HMGB2	702	-2.830279	0.1369618	No
ODAM	805	-3.875695	0.0166122	No
S100A8	808	-3.987699	0.0291392	No

• The Negative Phenotype (na_neg):

Table 5. Enrichment Plot of the Top 20 Gene Sets Ranked in the negative(Mock) Phenotype

194 out of 711 gene sets are returned in the Mock (na_neg) sub-type. 98 gene sets of them are significantly enriched at FDR < 25%. 69 gene sets of them are significantly enriched at nominal p-value < 1%. 89 gene sets of them are significantly enriched at nominal p-value < 5%. The most related gene set in this sub-type according to the analysis is CELL CYCLE REACTOME R-HSA-1640170.1, with an enrichment score (ES) of -0.56024605 and a normalized enrichment score (NES) of -3.6521144.

Figure 3. Profile of the Running ES Score & Positions of CELL CYCLE REACTOME R-HSA-1640170.1 on the Rank Ordered List

Figure 4. Random ES Distribution of CELL CYCLE REACTOME R-HSA-1640170.1

knitr::kable(CELL_CYCLE_REACTOME, caption = 'Table 6. CELL CYCLE REACTOME')

Table 6. CELL CYCLE REACTOME

NAME	RANK.IN.GENE.LIST	RANK.METRIC.SCORE	RUNNING.ES	CORE.ENRICHMENT
CDC14A	167	2.798065	-0.1873640	No
PLK1	409	-2.000453	-0.4754434	No
GTSE1	465	-2.089318	-0.5270098	No
CDKN2C	468	-2.096007	-0.5113444	No
ANAPC16	475	-2.104280	-0.5006769	No
CDC20	523	-2.200800	-0.5411358	Yes
CDC6	528	-2.216078	-0.5269628	Yes
PLK4	530	-2.221475	-0.5089405	Yes
TK1	566	-2.320188	-0.5331537	Yes
CDCA5	567	-2.322462	-0.5129871	Yes
FOXM1	575	-2.340321	-0.5015374	Yes
UBE2C	580	-2.349332	-0.4862072	Yes
RPA3	585	-2.365246	-0.4707388	Yes
CENPH	595	-2.395726	-0.4613429	Yes
HJURP	614	-2.451450	-0.4628700	Yes
CCNB2	623	-2.500282	-0.4512988	Yes
CDK1	628	-2.528634	-0.4344116	Yes
RMI2	635	-2.542336	-0.4199404	Yes
NEK2	637	-2.561090	-0.3989692	Yes
PKMYT1	643	-2.575518	-0.3829424	Yes
RRM2	646	-2.581340	-0.3630628	Yes
BIRC5	649	-2.603424	-0.3429914	Yes
UBE2E1	656	-2.633303	-0.3277302	Yes
CDCA8	676	-2.698342	-0.3283809	Yes
CDC45	681	-2.726066	-0.3097794	Yes
POLE2	682	-2.734335	-0.2860364	Yes
NCAPH	705	-2.854564	-0.2891329	Yes
KIF2C	707	-2.860460	-0.2655621	Yes
MCM5	714	-2.908502	-0.2479114	Yes
TOP2A	726	-3.004569	-0.2357636	Yes
SPC24	732	-3.025167	-0.2158324	Yes
ZWINT	733	-3.030731	-0.1895157	Yes
DHFR	735	-3.035134	-0.1644282	Yes
KIF20A	738	-3.066232	-0.1403381	Yes
NUF2	751	-3.151356	-0.1281831	Yes
NDC80	759	-3.269491	-0.1086652	Yes
OIP5	761	-3.282617	-0.0814288	Yes
CENPU	764	-3.303800	-0.0552758	Yes
AURKB	766	-3.351708	-0.0274395	Yes
GINS2	788	-3.632645	-0.0225122	Yes
CENPM	813	-4.064744	-0.0176351	Yes
SPC25	821	-4.366327	0.0114069	Yes

• However, this sample contains only 831 objects, which might be too few for the GSEA analysis.

3.How do these results compare to the results from the thresholded analysis in Assignment #2. Compare qualitatively. Is this a straight forward comparison? Why or why not?

These results do not have a threshold which is a cut-off according to p-value, so the returned gene sets are slightly different. It is a straightforward comparison. Because they are both imported from the same normalized data.

Visualize your Gene set Enrichment Analysis in Cytoscape

Visualizing the results from the non-thresholded gene set enrichment analysis in Cytoscape by Using Enrichment Map and AutoAnnotate.

1. Create an enrichment map - how many nodes and how many edges in the resulting map? What thresholds were used to create this map? Make sure to record all thresholds. Include a screenshot of your network prior to manual layout.

• In the Virus vs Mock gene set enrichment map visualization, we used FDR q-value of 0.01, p-value of 0.1 and edge similarity value of 0.375 as cutoff. We selected all NES. The Metric was set to 50% Jaccard combined with 50% Overlap. There are 339 nodes and 3033 edges in this visualized enrichment map.

Figure 5. Pre-Analysis Parameters

• Below is the over view of the network.

Figure 6. Overview of the Network

2. Annotate your network - what parameters did you use to annotate the network. If you are using the default parameters make sure to list them as well.

• We used the default settings of the AutoAnnotate application to annotate the entire map, we selected to layout network to prevent the overlap of the clusters. We used GS_DESCR as label column.

Figure 7. Pre-Annotation Parameters

• We selected a round shape, border width of 3, opacity of 20%, font scale of 20% and minimum font size of 4.

Figure 8. Annotation Parameters

3. Make a publication ready figure - include this figure with proper legends in your notebook.

Figure 9. Mock vs. Virus Enrichment Map

4. Collapse your network to a theme network. What are the major themes present in this analysis? Do they fit with the model? Are there any novel pathways or themes?

• The major themes that fit with the model include blood circulation heart,actin contraction filament, organism organelle organization, mitotic cycle sister, signaling cellular interferon, apoptotic programmed death, naba factor matrisome, positive cell proliferation, response biotic virus, taxis migration chemotaxis, programmed cell death, component movement migration, hallmark allograft rejection, activation involved neutrophil, viral life multi, negative regulation cellular, regulation metabolic positive, inflammation response stress, vasculature development, protein localization transport, transcription regulation biosynthetic, transmembrane transporter activity.

• There are also novel pathways and themes that do not fit with the model: epithelial mesenchymal, myogenesis, tnfa signaling, inflammatory response, hypoxia, muscel development tissue, extracellular organization matrix, estrogen response, oxidative phosphorylation, e2f targets, p53 pathway, interferon gamma alpha, uv response, kras signaling, g2m checkpoint and il2 stat5.

Figure 10. Mock vs. Virus Collapsed Theme Network

Interpretation and detailed view of results

1. Do the enrichment results support conclusions or mechanism discussed in the original paper? How do these results differ from the results you got from Assignment #2 thresholded methods

Yes, the enrichment results support conclusions and mechanisms discussed in the original paper.

2. Can you find evidence, i.e. publications, to support some of the results that you see. How does this evidence support your result?

Yes. The article can be found here. https://pubmed.ncbi.nlm.nih.gov/33805011/.

Reference

(A3_XinyiZhang.bib)